The looper I use is stereo (two channel). As these are discrete I guess you could incorporate each channel in each of your effects loops.This will keep everything separate, as it was before. I use it either for keyboards (stereo) or in conjunction with a pedalboard (also stereo), but if yours is for guitar alone, it'll maybe be mono, in which case my answer won't help ! As the good doctor says, any effect you want to loop/record will have to be routed through the looper.
Just realised you haven't bought it yet ! Consider a dual track looper - dearer, but probably more future-proof !