No problem. Keeping the layers separate is not entirely necessary, but it makes the editing easier. Same with using GIMP - just makes your life easier. You will want the layers menu enabled in GIMP.
There's a bunch of stuff you can do to make a fancier sight, but these are the basics.
BTW, the paths tool is your friend for making straight lines. To make a gun circle (like on the default sight)
1. Use elliptical select.
2. Check "expand from center".
3. Check "fixed aspect ratio, 1:1".
4. Click on the center dot, make the circle.
5. Go to Selection->Select Boundary (1 pixel is good enough).
6. Fill in the circle.
P.S., if your sight is all one color and very harsh, it may come out completely white in the game. If it does, change back to RGB mode and do Filter->Blur->Gaussian Blur (I use 1 pixel). Then change it back to indexed.