Assuming that the amplifiers for the P.A. are fully open, where do you put the master stereo fader?
Up to you. Where ever gets you to your required volume without feedback. I rarely go past -10db on the master fader.
To set a good gain structure through your system try this:
set up and turn on your PA including power amps but dont plug in your speakers to the amps. ( you dont want sound coming out FOH for this!)
Play pink noise through one of your channels. This can be from a computer/laptop/CD but not mp3 or other compressed file type.
With Channel fader at 0 raise the input gain until the channel is JUST about to clip with the pink noise.
Raise the master buss fader to 0 and it too should be just off clipping.
Raise the volume on your power amps until they clip, then dial it back till it JUST stops clipping.
You now have the same gain structure through out your desk and amps and you also know where you will introduce clipping but this should never happen on a system big enough to handle the room and its capacity because the volume you will have at 0db on the master fader will be far too loud for most people.
This will mean that your amps wont be 'wound right to full' as a lot of sound guys tend to do, but its better to not clip your amp than have it 'look' loud. You will get MORE volume from your PA this way as long as you set a good gain structure across your channels.
How do you deal with (let's say) a soft channel that requires a lot of gain to be put a decent level so you end up with it nearly clipping (analog, so it can be ok). Can gates and compressor handle very high or low levels?
Not sure I understand what you mean.
An active DI box can be good for this depending on the source.
Condenser mic?
getting something to near clipping does not sound like a decent level to me, thats sounds already way too loud in most cases.
Try getting things like guitar, bass, keys and other ryth. section type things set to 0db-ish.
The body of the drums set to round 0db with transients going to round +6db and vocals similar to drums.
Use busses to balance the instruments and channel faders for riding volumes of vox and soloists throughout the gig.