I can't remember there being any problems with roms, I remember a couple of games coming out pre-cracked with intros (One of the Donkey Kongs I think) but I never downlaoded a game and found it didn't work due to AP or incompatibility. Pokemon Gold and Silver used an internal clock that the cart didn't have, so I had to use
cheats to change the time of day, but that was about it. The program I used was DGBMAX - I can't find a link to that one, but apparently GBX Tool works as well and it's on filetrip It was programmed for Windows 98, so you may need to run it in a compatibility mode or something.
http://filetrip.net/f3013-GBX-Tool-1-8.html
Once I was up and running, programming the cart was pretty simple, but it's certainly more effort than it just appearing in windows as a drive and drag and dropping roms and saves.