I got started here:
If you look in the Platform Specific Series there's a few Neo Geo entries. Getting the development tools to work will take some tinkering, I believe one of the batch files in the toolkit has a typo that needs fixing as well. You'll also need a valid NEO GEO bios file and getting one of those isn't easy. MAME is a bit picky about NEO GEO emulation (even now I don't know exactly how it works or what file my game actually resides on, I just press F6 in Notepad++ and MAME automatically boots with my game in it)
For the graphics side of things, I use evobboy's NGGTS and YYCHR to edit my graphics. Sprites on the NEOGEO are split into two files, and NGGTS can combine them into one file temporarily for you to edit, then you can split them back up when you're done making changes.