If you have a multitude of PS1 and PS2 memory cards "created" ... it'll at the very least force you to set the ones you want up in Virtual Slot 1 or Virtual Slot 2 ... but just like a PS1 or PS2, if the game "searches" both slots, for the correct format card/save you should be good from there, and the cards that you've "left" assigned should "stay" assigned until you un-assign them.
A fine feature of the PS3 is that if you have the Memory Card reader/writer, you can actually write the virtual cards OUT to cards of the "real" variety.