I tend to put my octave box before any effect (not including tuner) so that it gets a clean signal to help with its tracking. However, pedals react differently and experimentation to find what suits you set up best is the way to go, as @uk_lefty says.
With regard to fx loops, I’ve never bothered them and stuck everything in front of the amp (this probably come from having amps without loops previously), it certainly cuts down on the cable spaghetti. However, as always, YMMV.
Ooh, nearly forgot