Jcook - what problems (behaviors) are you having? The standard way of using the two volume controls is to set the master volume around 25% (to start) then adjust the channel volume in each patch to be similar as you change patches. Then if you need more volume overall, you use the master volume.
For live playing, I would typically have a patch in each bank with the same tone settings as another patch, but with a higher channel volume so I could switch to that for a lead part.
Note that the amp has a maximum volume it can achieve - this is a combination of the 2 volume controls. If you have the channel volume at 100%, then when you adjust the master volume there will be a point where turning it further does not increase the volume any more.
If you bought a car and couldn't figure out how to adjust the radio and cruise control settings would you sell it? Or try to learn how to use it correctly?
Thousands of people have been using the Spider amps for years for studio and live work.