Agree with Hawkeye. The different SID types make thinks a little wacky, but after setting up your ensemble it should be good. Changing the LOG flag is the most important, but I also found that adjusting the min and max filter values was a big help. Just go by ear :)
Most of the circuitry in the MB-6582 is digital, so it’s pretty straightforward. If it seems to be working mostly as expected, ie changing patches, responding to input, proper LEDs lighting, then chances are that any hiccups come down to setting options in the software correctly. The synth engine is really complex, so it’s easy to miss something and get unexpected results!