How soon will I need to change from Bio balls to live rock rubble? This is what is causing all the junk in my filter?
Not "Causing" it but trapping it and raising nitrates. You have to replace them slowly, A Little at a time. Take a few out about every other day. Then when you get down to none, Add Rock Rubble back where it was.
You can use a prefilter sponge on your overflow box to catch most of the crap that builds up but it has to be cleaned quite often or it can build up the nitrate level from the trapped detritus.