what does it do to a bait if you get the ballist weight slightly off center when building a balsa bait?

makes it run like crap... or just spiral though the water.

If it's just slightly off center the bait will run just fine.   You may have to tune it just a little.  There will be a sweet spot in the cranking speed, if you go past that point the bait will blow out.   Slow to med speeds and the baits should remain stable.   Sometimes a little mistake like that can give you the magic action.   Finish the bait and fish with it, that's how you learn.