Some paintkits (the better ones) have all the detail like lines and rivets on a seperate layer. Unfortunately most don't, and its quite hard work to redo them all.
The chances are they will be the wrong colour anyway. If you are painting a white fuselage that has light grey detail with a dark blue then the light grey will be too much on the dark blue.
What I do (not necessarily the best way) is to use the magic wand tool and and select all of the lines and copy and paste them as a new layer. Then re colour them in a slightly different shade to the paint colour. You will have to experiment to get the best result. Keep exporting to FS and checking the reults. Sometimes after ajusting the alpha layer the lines are too much again and you will have to readjust. But good detail is what seperates the good repaints from the mediocre ones.
Regarding reflection, that is another issue, check out this tutorial,
http://www.calclassic.com/repaint.htmits using PSP but its basically the same.