I'm not familiar with the amp you're referring to, but I can give you some general guidelines to work with.
If you want to switch between two different sets of effect pedals, consider plugging your guitar into a 'Y' cable splitter that will feed both effect chains. Then use an A-B switch box to select which effect chain will be fed to the amp input. That, or look at some multi-effect boxes with programmable presets.
Most effect loops are active on all amp channels, because the effects are tapped into the connection between the preamp and the power amp.
There are a few exceptions. If you can get an old Peavey Rock Master tube preamp, you will find that each of the three channels has its own effects loop, plus a couple of loops for combined channels. Very versatile, though a bit confusing at first.
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