To switch between the GOW2 and COD5 game presets you have to reflash your controller with your computer. Unless you just want rapidfire, in which case I would suggest going to Downloads->Multi-mode presets->and download the Popular 5-mode preset. It has rapidfire only for COD5 and GOW2 in the same preset.
If you want the other fancy stuff (perfect reload, fast reload, etc) you will have to reflash your controller each time.
A little inconvenient, but not nearly as bad as having to buy two separate controllers, which is the case with mod shops with non-USB rapidfire products.
At some point we will be working on a 'supercode' in an attempt to put all the presets together in one big file but 1.) it's a LOT of work! lol 2.) we're not sure at what point we will stretch the capability of the mod chip.