The non overdriven portion of the amp is pretty standard stuff. Just note the passive mid and the treble work a little differently than you might expect. When dialing in your clean sound my suggestion is to set both channels the sound identical using the footswitch. Then set the gain and EQ on Channel A to the point where you think it sounds good, then A-B the two channels to see which you like better. You can keep doing the A-B until you dial in a happy sound. Then try dinking with Channel B and keep A-B'ing until you have a happy sound on B. I personally use B purely for heavy overdrive and leave A as my clean as I don't use the factory footswitch and instead switch channels using the Amp Ctrl jack on my BOSS GT-10B.
For the overdrive portion it's a whole different beast if you've never played with tubes before. Once in overdrive you can push a boosted signal to drive even more crunch, but not a lot more volume, out of the sound. Similarly, you'll find your volume and tone knobs on your instrument have a significant effect on the overdrive sound that comes out of the amp. Try playing your bass with the volume rolled off a bit, that leaves you room for a little boost right on the bass if that's to your liking. If you are an effect user, try pushing your effects into both clean and overdrive, you'll find some sound better or at least pleasantly different when pushed into the overdrive sound, for example synth effects and wahs/filters. Also, you might find some effects get eaten or sound poor into the overdrive since the amp's tube overdrive is now at the end of your chain.