I plan on removing my bioballs from my wet/dry a little at a time as I add more live rock but right now I have the water filled pretty high in the wet/dry so I can put my heater in it, will there be a problem if 1/2 the balls are under water?
The bioballs basicaly just provide a large surface area for bacteria to colonize. Your LR will provide even more surface area 8)
If the bioballs are underwater, it just means they don't get quite as much oxygen as if they're wet-and-dry. My pond filter uses bio-balls, and the bio-balls are fully submerged (ditto my former canister filter). As long as you get good water circulation through them, you're fine.
Why can't you stick your heater under the bioballs? Heater too long and you have to put it diagonally or something?
I could but it would push up the sponge letting water go under it instead of through it if that mattered? I also like to be able to adjust it w/o sticking my hand in the water or pulling it out.