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I've got a marshall valvestate 2000 AVT150H. The amp has 4 channels. An acoustic simulator, clean, O.D.1 and O.D. 2; and built into the amp you can hit effects for the 4 channels, there are several options like reverb, noise gate, flanger and so on, but I have to change all that at the amp itself.
So my question is: where should I put my multi effects pedal? Would it be better to run the pedal through the guitar and input on front of amp, or run it through FX LOOP?
The pedal you have (Digitech RP-90) includes amp and cab modelling, so one option would be to ignore the amp's preamp entirely, and run:
Guitar > RP-90 > FX Return > Power Amp
This is the setup suggested by the unit's manual:
Unfortunately, this means that the complex, multichannel preamp section of your amp ends up not contributing at all - just set it to clean and turn the FX mix all the way up.
The user manual includes the following signal path diagram, which shows the order the different effects are in and where the amp modelling sits:
Another option is to use only the effects up to and including the amp/distortion block (which you would set to either direct or one of the distortion pedals, not an amp and cab simulator), in the chain:
Guitar > RP-90 > Amp Input > Preamp > Power Amp
Or only the effects after that block, in the chain:
Guitar > Amp Input > Preamp > FX Send > RP-90 > FX Return > Power Amp
These options allow you to get fuller use out of your amp, but limit you* to one half or the other of the effects unit.
* By all means experiment with e.g. wah in the effect loop or reverb before the preamp, but effects generally sound "better" in the order Digitech suggest, particularly as a starting point.
Depending on the multi effect pedal you have, you can do both. But for the simple case, if you are using distortion from the multi effect, use it connected to your guitar. If you're using only e.g. delay or reverb use it in the loop. If you're using distortion in the amp, it usually sounds better if delay is applied on the overdriven signal, and not on the clean guitar signal. This is achieved by running it in the amp's effects loop.
For the "both" option, check out the 4 cable method.
