I know what you should put through them and what not to put through them, but what does it do to the pedals that are in the chain
it is used for a different sound purpose. Usually you have your OD/distortion/boost etc infront of the amp to push the tubes, then the modulation-esque type effects so that they arent affecting the tone thats going into the amp. Although thats not always what people do, everyone prefers different sound and i guess its just a matter of testing and playing around with it. But usually modulation comes after distortion
i mean the modulation effects if your using the amps distortion you wana put things like delay and chorus etc in effects loop
it doesnt need to be, it depends on what you think sounds best, if that is a modulation infront of the distortion then other modulation effects in the loop, or all modulation effects infront, its entirely about what you think sounds best and like. But most will say, me included, that modulation should go in the effects loop. At least thats how i do it
Also time based effects such as reverb and delay pretty much need an effects loop, distorting reverb amplifies the effect so its impossible to get a subtle effect no matter what setting, it always sounds like youve put you amp in the middle of the grand canyon or a my bloody valentine set up.
The reason for using an effects loop is to have the pedals in it, used after the preamp.
MESA 412
Guitar -> Wah -> Distortion/OD -> Preamp -> Modulation/Delay/Reverb -> Power amp -> Speaker

The point of the fx loop is to be able to put effects between the preamp and power amp.