Dave, I'll give you my take for what it's worth.
All special effects like verb, delay, chorus, flange, and the like, are better when put in your effects loop because you want those effects to be clean.
Effects like eq, compression, pitch tranposer, wah, volume pedal, distortion, etc, are best in the front of the amp because they are primarily "dirty colored effects". If you put them in a loop, it would be like putting a distortion box directly into a mixing board.
Now with your current situation, if the modeling pedal is supposed to be in the loop, then that's where it should go. The Boss CS 3 could be placed in the loop or in the front. Though that contradicts what I said up there, I don't know how the modeler works and you may very well need to compress it through the loop. You'll have to experiment and see if you need that. The delay I would definitely run through the loop.
Your best bet is to experiment though because every pedal and situation is different. I'll tell you my reasoning for the above advice though just so you know the method to my madness. Let's look at the front of your amp as a channel in Sonar. Any effects that you put into the front of your amp would be equal to you putting effects into your FX bin on a track in Sonar. This often times makes the signal a bit dirty when you use verbs, delay, chorus and the like. You're better off when you put those effects in a bus, create a send and then insert a send on the track. With me so far?
Ok, when we go into your effects loop in your amp, it's the equal to creating that bus and inserting a send to a track. You're working off of two signals now. You have your dry/driven sound, and then your uncolored, effected sound. This makes reverbs, chorus, flange, phasor etc more lush/transparent without the dirty part of your signal chain dirtying things up, understand? So that's why I wouldn't normally put a compressor in my effects loop. It would be like using one as an effects send and I normally do NOT like to do things that way because 8 times out of 10, a compressor is going to sound its best in a guitar rig in the front input instead of the effects loop.
But because you have that modeling thing going on, I have no idea what your needs may be...so that's why I'm saying experiment a little. But a good rule of thumb for me has been what I've shared above. Good luck! :)
-Danny