Ok, first off, haven't painted any miniatures since I was in high school (along time ago) and decided I wanted to try my hand at it again using my x wing stuff. Have just a couple questions for those of you with a lot of experience. I painted right over top of the factory paint job with citadel paints and even after a few coats I still have some obvious brush strokes, do I need to water down the paints a little more/less? Also, after you paint, what do you use to seal the ships so the paint doesn't come off from being bumped around a lot?

I wish there was a painting sub forum to make it easier to find answers to stuff like this....

First off it kinda depends on the paint you're using. Most people these days use water based acrylics, I myself use the Valejo brand. The Valejo range has a wide choice of colours as well as mediums, washes and varnishes. The mediums (clear liquid in all kinds of finish like matt or gloss) are great for making the paint more smooth. It also depends on the amount of paint on your brush and even on the quality of said brush whether you get brushstrokes or not.

judging from your story my first question would be whether you cleaned of the mini's before painting. I do not mean whether you stripped the paint, since you stated you didn't, I mean you have to rinse the mini's in soapy water and get them totally dry before painting in order to do away with residue mould- and hand grease... if this is not done properly the grease will prevent the paint from properly adhering to the surface.

also be sure to check youtube for tutorials of many of the great painters on this forum. Many of us also show a link to their blogs with repaints in the signatures worth checking.

I painted right over top of the factory paint job with citadel paints and even after a few coats I still have some obvious brush strokes, do I need to water down the paints a little more/less? Also, after you paint, what do you use to seal the ships so the paint doesn't come off from being bumped around a lot?

If you can see brush strokes (but not the underlying color), then your paint is not thinned enough, you need to water it more.

Best way to seal the ships would be some kind of varnish, I use Vallejo Model Air matt varnish applied with a brush on my minis.