How did Angier know not to appear in The Prestige?

I guess he just recognized Borden from the people examining the apparatus while he stood in it and assumed that he will probably walk behind the stage (or maybe even saw him do that).

The fact is, that Angier was at that point in time so much sunken in his wrath against Borden and the desire to know how his Trasported Man worked, that he didn't just do those Real Transported Man shows to make a good show and beat Borden success-wise. He actually planned this "murder" to happen some day to finally "win" against Borden, since he knew he would show up one day to look behind the stage and nobody would doubt that he murdered his enemy. But even if at first Angier looked like the one that always got framed and played wrong by Borden (and finally murdered, as is shown at the beginning of the movie) it was actually always Angier who took this fight from a job-related competition to a higher level, involving kidnapping and finally murder. This is also to some degree evident from his dialogue when he says:

Cutter: What kind of booking are you after?
Angier: The one that Borden can't ignore.

So he was prepared for Borden to show up some day and just needed to look out for him, the rest was already planned out perfectly.

I thought the clone just stayed hidden and observed the audience for a few second, to see their reactions. (There was always a pause between the disappearance and the reappearance) Since when Borden found his dead body, he started shouting, which everyone in the audience heard. So the clone just waited and heard if Borden was shouting. If yes, he now knows that he found his dead body. If everyone just looks amazed and no sound of Borden, the clone will appear and repeat the same process next time. I think that's why he arranged 100 performance because he doesn't know when Borden will show up.

See on this my opinion is that ANgier did this whole setup - 100 shows of 'The Real Transported Man' to trap Bordon. He knew that one day Bordon will come up the stage disguised in some form and he will go below the stage to see what's happening. This is also evident from one scene when Bordon goes home after he first sees Angier's trick. He says it there "What's happening beow that stage". So when finally that moment arrived - when Angier is performing the trick and someone from the audience is called up on stage Angier identifies Bordon and the he knew that now is the time, not to appear, because this will leave Brodon with the dead body in the basement. –

So here is my grand theory (if I understood the question correctly):-

Angier was Lord Coldlow from the very beginning. He just pretended to be the American Robert Angier, to spare his family the embarrassment of his theatrical career. So existence of Lord Caldlow is clear.

Later on the day of the accident, Angier called spectators to check the machine. Borden came and examined. Given the fact, they knew each other the best, we can assume Angier caught him right then when Borden was on stage to check the machine.

So when Angier understood the right time has come, the time he has longed for a long time, he did not turn the machine on simply i.e. no extra copy of him was made on that day! But he tried to befool the viewers by the sparks of the machine and all that, but it was not really working like other days. So the existence of Angier remained as Lord Caldlow (whom no one identified as him) and Angier could make Borden his murderer by killing a copy of himself, the then present person in the centre. Simple yet a compact plan!

I don't think there was enough time to get the message across before the prestige that Borden had just shown up. Instead, my theory is that Angier faked using a double as part of his act along with faking his own death. This way, it explained a dead Angier and a living look-a-like.

It's not clearly shown in the movie whether Angier saw Borden moving to or behind the stage as there was no eye contact shown. One can only assume that Angier knew some how that Borden will go back stage, the cloned Angier didn't show up to place the blame on Borden. I believe this is a way in which the writer/director keeps the audience occupied in the movie. Similar questions arise in the movie named "Shutter Island" in which the movie ends with the saying "this place makes me wonder whether it's better to live as a monster or die as a good man"