so here's an example.

in a real tube amp, the gain control affects the preamp gain.  the master volume controls the amps overall volume by allowing the power amp tubes to amplify the signal to be louder.  a side effect of that is the harder the power tubes are driven, the more they distort and compress.  but when you're using a full amp model, the power amp distortion is modelled, so turning down that master control can make the amp moddle sizzle less, try the JCM800 amp, and from defaults, turn the master vol and gain down to a quarter.  then put a tube screamer in front of it.  that sounds to me a lot nicer than the amp model defaults.

there are other effects, like in some amps when you push them very hard the initial attack of the note is more in your face, and then the power to the amp (through the transformer) sags and the sound is a little more 'saggy' and loose. that's the sag control.

hum... who wants hum... right...... actually wrong.  the audible hum in a tube amp (that sometimes happens) is not what we're talking about here, although that can be a side effect.  ripple from the power supply is smoothed by filter caps, and the ripple left to go to the amp can sometimes (in small quantities) make an amp sound more alive.  if you're using a very well designed power supply and there's very little plate ripple, then the amp can sound more sterile.  too much hum the amp comes alive but you hear the audible hum.  middle ground is best, but some amp models in the POD you don't ever hear the hum and you can turn it right up to have a slightly more synamic amp.  this is because some real amps don't suffer teh side effects.

bias is how hot you're running your tubes.  turning it up you get a more smooth tone, and the background distortion (which can sometimes sound a little fizzy) is gone, as you're running in class A.  turn it down, and it sounds more raw.  in a real tube amp you can't do this so easily, it's an internal amp job. 

here's something I copied form another thread replied to by Crusty Old Rocker, as he explains it better then me:

"Bias excursion, as the name implies, is movement of the bias.  Driving power amp valves hard actually has an affect that moves the bias and it takes some time for it to shift and to return.  It simple terms the bias on a pair of heavily driven valves can shift toward a lower bias and introduce more distortion to the power amp valves.  Having control over this could make it occur at various levels lower or higher which would result in the characteristic being introduced at a different point."

presence is a standard control on most amps, and it is basically a tone control for the overall amp... kind of.  but that's how I'd view it in a simple context.

so if you want a more vintage, smopoth sounding amp, turn the hum up a bit, bias and bias ex up, sag up, master up (or down) and away you go.

if you want a more sterile high gain sound, sag, hum, bias and bias ex turn them all down to taste, and master up or down to taste.

Enjoy

Rowbi