When you first prime a textured ceiling you need to use a non-water based paint. If you don't, the stipple will soften and come right off. After it has been primed with oil or whatever, you should be able to paint it with latex. You can only paint latex over the oil primer or a latex primer, not an oil paint. I'm not sure about a spot that has water damage, but you can't go wrong painting an oil primer over whatever you have, then using latex if you wish.
Make sure you use a very fluffy roll and you should have no problems at all.