Do different roms affect aftermarket programs?

[Modsport]

This may be a silly/stupid question, and if it is please excuse me as i'm still new to this phone and learning all the different things about it, but ive read about different roms, and how they help increase speed and battery life among other things... My question is after installing a new rom, will i still be able to install SPB Shell on it since i like the interface, or after installing a rom am i just limited to whatever interface it comes with? Just wondering if it affects what aftermarker software i can still use if possible after flashing, or does it not matter... thanks