Did Natalie really help Leonard or was she just using him again?

This is indeed quite a good question and I cannot do much more than recapitulate some speculative things you might have considered yourself already, but let's see.

First of all to some degree Natalie serves as a distraction to prove that notes are in no way less treacherous than memories, by being presented as "good" while being revealed to be more and more "evil" later on, and thus opposite to Teddy. But still you are right in that she couldn't know about Teddy being the one with the license plate, so either it was a writing inconsistency, sacrificing a bit of logic to the purpose of a nasty revelation about Natalie's character, or we can really find some justification for her actions later in the story (earlier in the movie).

But even at the beginning (of the story -> later in the movie) she showed some compassion for Leonard during his first visit in the bar, when she was about to play a little trick on him with the beer everybody had spit in. She takes the beer away from him once he starts talking about his dead wife as she probably feels a bit guilty seeing that Leonard really got some serious problems.

And while the scene where she got beaten by Leonard and revealed her bad side probably didn't show her from her best side, she was really at a dead end herself at this point, with Dodd chasing her for Jimmy's money and her not knowing if to trust Leonard or if he had anything to do with Jimmy's disappearance. So much of her bad bevahiour in this scene could be seen in the heat of the moment (and maybe even with the intention of provoking a punch from Leonard in order to blame it on Dodd). So I think even then she didn't misuse Leonard just out of bad will or greed, but because she had serious problems herself and was not lying when saying she was threatened by Dodd, even if making up the beating.

Now when Leonard arrives at her house after beating up Dodd she indeed first eagerly and selfishly asks if he killed him. But then she starts to see his "freaky tattoos" and learns a bit more about his dead wife and especially his deep feelings for her and his determination in finding the killer, to which she says "I've lost someone, too". And later they share a night, with Leonard talking very emotionally about his wife and his quest for revenge. And indeed the next morning Natalie says she'll check the license plate. And I think Natalie's behaviour during this whole visit seemed very honest. This is then also continued by her honest enquirings about his memories of his wife, when she gives him the information about the license plate in the bar. (Yet, this is all shown before the reveal about her misusing him later in the movie, so it's maybe hard to say in which way we can trust her depiction entirely or in which way it's deliberately distorted to facilitate the effect of the later revelation).

So while being revealed to have rather bad intentions later in the movie, I think especially this visit by Leonard indeed sparked some feelings in her for him. If not actual emotional feelings for him, then at least understanding of his situation and his quest for revenge, maybe mixed with guilt about misusing him. So I agree with the fact that she's a much more ambiguous character than one (at least I) might think after watching the movie just once and I'd deduce that she really wanted to help Leonard when she checked the license plate, not knowing that she would also find the man responsible for Jimmy's death.

So while we might think to have been misguided by Natalie's earlier (in watching order) nice bevahiour once her misusing of him is revealed, the actual story development if seen in chronological order draws a nicer or at least more ambiguous picture of her character.

The first time around Natalie is in a fix.
- Her boyfriend Jimmy is gone leaving her with a debt to Dodd.
- She sees Lenny with Jimmy's car and clothes.

Natalie chooses to use Lenny because she knows that he has something to do with Jimmy's disappearance. Also she mentions that she is a survivor and all she's doing here is surviving.

So yes, the first time around she's using Lenny to get rid of Dodd for her.

She notices the Tattoos on him and Natalie understands the pain that Lenny goes through every moment of his waking life. Natalie says that she lost someone too.

Later on, she understands the kind of pain that Lenny goes through. She associates it with her own loss (Jimmy).

Natalie only knows the name Teddy, she has never seen him. She doesn't know Teddy is a cop by the name John Edward Gammell. Since Lenny never takes out Teddy's pic in front of Natalie she is in no position to connect Teddy and John Gammell to be the same person.

She has traced the number plate to a guy called John Edward Gammell. She doesn’t know that this guy is Teddy. Lenny doesn’t check his photos so he doesn’t talk of Teddy either. Natalie has grown to like Lenny for the love he displays for his dead wife.

Natalie is not using Lenny the next time around. She's actually helping him out. When she gets the License Information. She gets him John Gammell's Pic and Details. Natalie doesn't know that this is Teddy. Lenny also doesn't make that connection till he gets back to his room.

She also adds an address where he can take this John Gammell and finish the job. It’s the same address where Lenny kills Jimmy.

This address is where Jimmy did deals. That is all that Natalie knows. She has no clue that Lenny has killed Jimmy at this location. Lenny doesn't remember either. So even the location that Natalie gives so that Lenny can kill Teddy is purely coincidental.

To conclude, while Natalie used Lenny the first time, the second time around she's honestly helping him because she does feel sorry for him. She doesn't realize Teddy and John Gammell are the same guy and is unaware that she's getting her revenge.

I think both is true. At the same time I believe she's doing it all out of self-interest. Having seen the movie 7 times (or so) I'm convinced that Natalie is a person which is rotten to the core. She's absolutely playing Leonard in every minute because she knows about his condition and because she knows that he is a chance to get out of her quite bad situation after Jimmy's death (Dodd and maybe several other people having her suspected to be responsible for it). She knows Teddy because Jimmy knows him, too. So I think it's not improbable that she even knows his license plate. Teddy was a cop on an undercover mission to set up Jimmy and already managed to get some of his trust, so I suppose that he and Leonard are around there for quite some time. Natalie didn't figure out that Teddy was a cop, but as a supposed rivalling drug dealer he posed an even bigger threat to her after Jimmy´s death. She needed to get rid of him.

Natalie is a cold and calculating person - don't forget that she is the girlfriend and business partner of a drug dealer. She does never really mourn Jimmy's death, instead she's rather looking forward to snap out of her situation. This is where Leonard steps in. First she gets really angry at him because she knows that he effectively killed Jimmy. But very soon she realizes that she is better off using him to her advantage. This is why she is being very nice to Leonard - in the end she knows, that it would stick in his notes (which is all that counts). All the "kindness" and "compassion" she shows is essentially false and just a trigger to get Leonard to kill Teddy, which is a - at least supposed - threat to her.

So why do I think Natalie helped Leonard? Because she contributed to him getting finally rid of Teddy. Her motives may have been far from noble, but in the end it may give Leonard's life a turn for the better. Teddy had been the curse of Leonard's life for many years, turning him into a serial killer and very probably preventing him from seeking medical/psychological assistance which he urgently needs.

If you start watching the movie assuming that Leonard is faking, everything falls into place. It makes it very plausible that:

1. He was involved with the drug dealers

2. His wife found out.

3. He hired them to kill her.

4. When it didn't work he concocted the story of having amnesia.

5. Used his experience with Sammy's fraudulent case to learn how to not make the same mistakes.

6. Stayed in character, even with self-speak, so as to pull it off.

7. If Dodd wasn't scared of Leonard knowing he was a hard core killer and previous knowldege of him in the drug trade, why would he leave town "for good"? Dodd was Jimmy's boss, period.

Higher up in the drug trade, are we supposed to believe that he is afraid of an insurance investigator who got the jump on him and beat him up? He would send people to take care of Leonard unless they knew who he really was.

He had to kill Lenny in the end to end the farce and go on with his life-with all the money mind you. Everyone else that knew of his former life as a drug dealer and that he conspired to have his wife killed was dead.