well some tips that might help. re arange the UV mapping so that you end up with less seams and usualy try to get the seams on either a side you will never see or along an edge where a seam is easy to hide.
make a base filled image ( not showing the poly lines ) off of the poly mapping image. Layer them so you can see through one to the other ( solid filled aeras on top of the poly line mapping). you can then select one smaller area and then work that one piece, little area at a time, on its own seperate layer. some areas your texture may end up with several layers in itself to get the desired results.
don't rely on one paint program to do it all either. I use Gimp, Photoshop Lite 5.0 ( free version), dogwaffle, Pixia ( tehre are many others free to use)
each can do a few things easier or better than others, and most will allow you to move the image around in photoshop file format so can keep the layers.