It really depends since some program will let you install on SD/CF while others requires that you install them on main memory. You'll have to contact the developer to find out.
If you were to have a choice, I'd say store it on your CF since it'll be faster than on filestore.
As for the brand, there are a lot of mixed reactions so it's tough to say. I've tried a few (Kingston,PNY,Lexar,Sandisk) and I've yet to face any problems but with others, some failed while others are sworn by.
Enjoy your PPC, mate.
