Essentially, you can set up your rig how ever you choose (pedals in front or in the loop) without the TMP, then just add in the TMP as mentioned above, and retain your entire rig as it was, switching between that and the TMP with the side track.
Say your rig is as follows...
Guitar>TS808>Gate>AMP IN...FX Send>Delay>Reverb>EQ>FX Return
You would simply run your gutar into the TMP guitar input, run a cable from the Sidtrack send to the TS808, run the cable from the EQ in the loop to the Sidtrack return, and run a cable from the TMP output to the FX return. This way, when you engage the Sidtrack, you have the same exact rig as before, with the guitar going into the TS808 and the EQ going the the FX return on the amp.
This gives you two distinct preamps. You can also run what ever you want in the Sidetrack, like a Digital Modeler, or another preamp, and do the same thing.
It's an amazing device, and I wish James would make it into a rack mounted preamp with the same features.