Running my AT853's > R09 is probably somewhat similar to your Squids... run it as required to get the gain you need at the time. I don't think there is one right answer.
At a normal "loud" show, I run Mics > Batt Box > Line in, with gain set frequently in the 15-20 range. There is enough drive here that I don't need any additional gain mic preamp gain, so I just run line in...
If it's a quiet, typically acoustic, type show, I would run Mic-In (low sensitivity typically). If I where to use Mic > batbox > Line in as described above, I would have to run line in at a full 30 gain, and still have low levels. The preamp exists to be used, so I use it in this case.
I have run my Nak mics (which are well known to have very low levels) into mic input on HIGH gain, because I need the gain.
I don't typically use AGC... I just don't like it... but that's preference.
Joe