Ditch MS Paint, work in Photoshop. Seriously, there are a few things you need to know. One is the general tools. Playing around will teach you what you need to know.
The second is the layers. In RGB mode you get layers. Click the "New Layer" button in the layers window. You can click and drag them around, the ones above will be "on top" of the others. You can right click and find lots of options for a layer.
Work in layers. Put a part of it on a layer, like panel lines only on 1 layer. Then color in the green of the SEA camo on 1 layer only, for example. Then put the grey of the SEA camo on another layer, for example. This way you can adjust the panel lines as many times as you want without having to re-do them all the time over and over, which is what you have to do in MS Paint. Just don't work in paint, ever
EDIT: One layers tip: Take the default image (the file AH gives you when you "save default skin as...") and put it as your bottom layer. Then don't touch it. Work on other layers. That way you don't have to re-do landing gear and stuff, and can just focus on the important stuff. This helps when you are still learning the tricks of the trade.
