Hi Daniel - I just happenned to find this question as I checked my messages on here and I hope you don't mind me chiming in.
I have spent many years working with mics and amps for harmonica, and aside from being an amplified harmonica performer, I have been re-building vintage harmonica microphones for over 20 years and love to continue to do so (and played through hundreds of amps and literally thousands of microphones). One thing to remember is that every microphone/amplifier combination will soundand act differently. Unfortunately this means that there is really no "standard" of how to set up amps for harp, also because each players' microphone cupping technique is different, and the cupping also makes a huge impact on the amplified sound (and how you should possibly change the settings).
As a starting point, I usually start with the volume on 0 (always a good place to start, haha!)...if there are separate tone controls I will set the treble somehwere between 3-4, and bass between 6-7 and go from there. If there is just one "tone" setting, I would set it at around 3-4. All the other controls (there may be no more, or possibly up to 10 more depending on the amp) can start to confuse things or may not be all that important just to get a setting to start at. For example, "reverb" or any effects will not be needed just for a good tone/volume. However any "master volume" or "gain" controls (if there are any) may interact with the normal "volume" setting depending on the amp, and in turn make things a little more confusing.
When using a microphone with a volume control, I would make sure to set it all the way up (or close to all the way up, if you want a little room to crank it full blast for a boost here & there).
This comment is already loger than I originally intended (sorrry!), but maybe it gives you a little help in understanding my thoughts and understanding the overal amplified harmonica thing. Remember that each mic/amp combo will act differently, but the above is basically my recommended starting point. I also agree with Larry that spending time yourself with the equipment will help you get a handle on working with it, and to find the correct setting for yourself and your equipment.