Default Formatting int and ext storage

I have a lot of built up trash on my cards from different roms and apps that I don't use anymore. Will wiping the cards cause issues with apps I have? And will I have to sbf afterwards since the system files are on the int card?

Sent from my Eclipsed and ICS themed X2.
T3HBR1AN
Moto Droid X2
CyanogenMod7: ICS Style