-Does the level of the pokemon you fight or how fast you reach the next level matter in EV-training?
No. EVs are completely and utterly separate from XP.
-If I wanted to get 255 points in Sp.Att. and 255 in hp should I first fight 255 spindas and than 255 whismurs or can I let`s say fight a whismur than a spinda than again a whismur etc. till I reach 510 points?
Since 255 is the maximum you can get in a single EV, you can beat up Spinda and Whismur in any order you please. Once you reach 255 in an EV, defeating more of that pokémon has no effect whatsoever on your EVs.
-Does depositing or healing during EV training do anything bad to the stat points I get?
No. In fact, depositing might be a good thing, because it forces the game to recalculate the pokémon's stats then and there. You can see what effect your training thus far has had on your pokémon's stats.
-Is it true that youget 1 stat point for every 4 ev points you got? This would mean my rayquaza should get +63 points in Sp, Att. and in hp?
Only at level 100. It's a percentage thing.
Also what evs would you recommend? I thought about 255hp and 255 sp. att. is this any good?
As far as Special Attack, it depends on your moveset. Certainly feel free to boost special attack if you plan on teaching Rayquaza mostly special attacks. If you're shooting for level 100, though, you might not want to go for the full 255. After all, as noted earlier, at level 100 4 EP = 1 stat point, and it doesn't round up. So you get 63 stat points, and 3 wasted EP. It's common to put only 252-3 in your two maxed stats and put the leftovers in a third stat to get one more point out of your EVs.