Well, amp settings depend on the amp! There is no set 'do XYZ for a great tone'. I can explain it to you in terms of frequency, but if you're not conversant in frequency bands, it won't help much.
Marshall EQ is passive, meaning that you would want to start with the settings dimed, and then add attenuation from there.
Does your amp have a valve in the preamp? If so, you should set the amp to the point where you're getting a good crunch, not dull-on distortion, and then add the OD, as clean as possible at first, then raising the gain until you have the desired gain.
If it sounds tizzy, roll back the Presence first, not the treble.
You don't want too much bass, it makes everything muddy and gummy sounding.
My personal rule of thumb is to tell people to set the midrange until you just thing that it's a bit much, and then add a bit more.
This should yield a tone that will sound good atl all levels.
Oh yeah ...
ALWAYS set the amp up with the effects turned OFF. After the effects are added, adjust the tone as needed.