GBE+ won't let you edit the ROM, it works by replacing the graphics you see on the emulator.
If you really want to start a colorization project I'd suggest you to try and learn GB ASM. It's a difficult task but not an impossible one. I'll make SML2DX's source code available and try to document the first steps of a colorization project, so you can use that as a base.
Also, keep in mind the system limitations when making a mockup - backgrounds can have up to 4 colors per 8x8 pixels block (using up to 8 different palettes) and only 3 colors for sprites.