Help me understand the interaction between Marcus and John Wick

Marcus was given the contract to kill John Wick. Then the next thing we know that he was helping John Wick. Question is why? Did I miss anything?

You did not miss anything. As already mentioned in the comments, Marcus helped John because they were good old friends. One way of knowing that is that Marcus is shown attending John's wife's funeral at the beginning. As to the "Marcus helping John part", it's because, at the last moment, Marcus chose friendship over money.

They must have been communicating, otherwise Marcus wouldn't know when and where John will be.

No. They were not communicating. Marcus knows that John is at Hotel Continental because that's where all the gangsters reside when they're attending business and John is staying in the same room he used in the old times before he retired.

John wasn't worried about the first shooter, he was fighting Perkins as if there is no other killer. So John knew Marcus is helping him.

No. If you re-watch the scene again, you'll notice that John knows that someone is shooting but his main priority is to deal with Perkins who is an immediate threat to his life.

Even when they meet after the saving of John Wick for the second time they don't discuss really why Marcus helped him?

It doesn't matter. As the main villain mentioned in the beginning, John Wick is sheer will and focus. I'm guessing that John is intelligent enough to understand that Marcus took the contract for money but for the old times and Friendship's sake, he changed his mind.

I joined here just to answer your question because I find the movie really cool. Here's my opinion. Communication isn't necessary at all. Viggo said they're "close" so yeah it's granted that he knows John's every move. When Marcus made a deal with Viggo, he's been betraying him(Viggo) all along and has been covering John Wick's back. When he's about to come into the Continental, Marcus has been watching over him. In the hotel that night, that shot isn't missed, it was intentional (there's no way a serial killer would miss a shot on a sleeping person's head even though it's John Wick), why? he saw beforehand that there's someone else in that room, and he shot his pillow to wake John Wick up. He didn't shoot that Perkins directly maybe because imo he respects John Wick to take care of her and yeah he fought in the Hotel without worrying anything because he knows he got his back covered by his friend Marcus.

Edit: I don't think Marcus is related to Helen(John Wick's wife) like the other person said. In the burial, he asked, "Marcus what exactly are you doing here.". I think it would be really rude.

Well, i think that John stole Marcus wife Helen and that why Vigo said I think you would find it personnel. But at the end, Marcus respects that John really loved his wife and respected the fact of her passing. And that's why Marcus's was at the wedding in the beginning of the movie that's why John asks what are you doing here.

What I was thinking is that Marcus was offered millions to kill him, yet someone else was doing the killing, meaning he wouldn't get the money. So by rescuing him, that gives him a new opportunity to follow through with the original contract. This is what I thought at first, but then they met again and were cordial. He didn't try to kill him, and told him it was time to go home. Then, the other guys must have known that, because then they killed Marcus, and this was also to get that guy's anger out about his son. It appears that the student's skille exceeded the master by that point, or did it? Because John Wick's timing was not enough to save Marcus, the way Marcus had saved him; food for thought.