If your using MS Paint, you can have 'draw Opaque' on in the "image" pulldown from the menu and the color that you use for the right click (your secondary opaque color) is the one that won't show up in GE. So if you do what CAAZ says, it will work. You just have to use the opaque color to remove the outlines of the frame. By using squares that connect that are the same color, you can just use "fill image" (the bucket) and all the reference lines disappear. In this case, the second color would be white. Without using a reference, your animation may shift from side to side or up and down during it's sequence.
I use alot of different tools, but Plastic Animation Paper 4 is another way to create animated strips.
http://www.plasticanimationpaper.dk/
It has a free unlimited trial, though you can buy it if you want. I'm still working on my scripting, but I have concentrated on the animation aspect until I get everything down.
Hope this helps.