This is a broad topic, one thing I've noticed is that everyone has their own unique setups (surprise surprise
). You can run pedals in front of the MP1 but need to be careful (as anytime you run pedals) with the gain structure (ie which order you put them in). Depending on the pedal, you can run them in the loop but again gain structure is the main issue, pedals are generally designed for guitar level signals (millivolts) and the loop and rack effects generally line level (~1 volt). Mixing rack and pedal gear creates major gain miss matches but you could, for example, use some pedals in front and a rack effect in the loop (eg wah pedal in front, decent delay & reverb rack unit in the loop). If you just had pedals in the loop, the MP1s loop has gain adjustment but I wouldn't do it that way. When I bought my MP1 I wanted to get away from pedals so it was all tidy in a rack. Also rack effects are generally much better quality (& more expensive) than pedals, they also generally can be controlled by MIDI so everything changes at the press of one button.
I started a thread a while ago about how do you connect your gear, there are some good ideas in those posts (http://adadepot.com/index.php?topic=117.0). There's also a post from MJMP with pictures of his rig(s), I can't quite find where it is though. MJMP has a pretty full pedal board which I assume he runs in front, some setups can get fairly elaborate.