The bioballs will work fine for fish only, at least in my opinion. You could slos out live rock back there, thats what i did initially. I just love the convenience of the baskets and I wanted a fuge so thats why I did the upgrade. It's by no means necessary.
I would think it'd be better to switch the media right off as if you do add live rock back there you want the beneficial bacteria from your cycle to be there too. If you start with bioballs and change later you have to grow a new colony of bacteria in that section. Also, you could slowly change out the bioballs for live rock rubble over time so as to not disturb the balance of bacteria.