Skin editing is kinda similar. Once you've extracted the WTP into the separate TGA images then each one represents a layer of colour. Paint an area black on the Primary layer, and you won't see any primary colour on that point. Paint it white and you'll see pure primary colour (or possibly white - I've had a few problems using pure colour!) if you paint it a shade of grey then the further away from black it is the closer to pure colour it is. Dirt is slightly different, but I'll leave that until later, unless you're planning on adding/removing team colourable areas already
I might have mentioned them already, but read the
Dawn of War Skinning tutorials on the main site and they should cover most things
if you read and work at the same time it'll be easier, and if anything still doesn't make sense then post back and I'll try to clarify and improve the tutorial
[edit] Oh, and if you want to copy things and mirror them then the best way I've found in Photoshop 6 is to paste them into a new blank image (new images automagically have the correct canvas size) and then use Image > Rotate Canvas > Flip Horizontally then copy and paste back again
there is probably a way to get it to apply just to the layer (doing it without going into a new image) but I haven't found it yet.