Hi Chris
In general you want a nice strong low-noise signal at the input of any stage which has gain, as everything which is fed in will be amplified by the same amount, including any noise present. Provided the instrument pre-amp itself isn't clipping (get your gtr/mando/banjo player to play as loud as possible in the sound check to make sure) you can always reduce the signal level at the mixer input.
As regards different parts of your PA system, ideally you would set all the input levels so that everything in the signal path from mixer input through to power amp clips at the same point, to achieve maximum clean output with minimum noise. If you had already set the input level of your power amp so that it clipped at the same point as your mixer output, then anything you put in between should have unity gain to maintain your gain structure - however the thing you've inserted (GEQ, whatever) would also need to be set up so that it clipped at the same point. If all the units operate at the same sensitivity standard (i.e. 'pro' or 'consumer') and they all have decent headroom, it should be easy to set everything up together.
It's often neater to put things like external GEQ on a mixer fx send/return rather than in series with the main output as it's more flexible and it's one less thing to go wrong in your main signal chain - if something goes wrong it's easier to bypass an fx loop than start unplugging cables.
Hope this helps a bit
Mike