hi,do you mean you weren't using the gravel vac properly? this is like a siphon and you stick it into the gravel, it sucks out the much as well as the water. i hate using them, i can't get on with it at all i create a big mess of water everywhere and the water goes horrible for hours after. so i have decided to just stop using it. i haven't cleaned the gravel for ages and i haven't had a problem with ammonia so that's probably not why u have ammonia. it might just be the fact that you have too much waste in tank eg food for bacteria to process. how did u cycle your tank? with or without fish?
anyway, you can do water changes 2 days running at 25%, you should probably increase this though if you have high ammonia. do you have a test kit? if so whats ur ammonia level? if its above 0.25 you should try to lower it. same with nitrite