Alright I'll try this.Yes. You can either patch your ROM before injecting it (you will need to add all of the game info and icons yourself, since the database does not contain hacks) or you can load a vanilla ROM and select an IPS patch to be applied during the CIA creation process. I like this way better because the data from the unmodified game is found in the database and loaded automatically, so you only need to change a couple of things.
Thanks for your help so far.