I have a pre amp and a power amp in my rack (rather than a head combing both), and I currently have my FX loop running through the Pre amp's FX loop. Does it make more sense to run an output from my pre amp into my FX loop and then into the power amp?

that would mean placing it in between pre and power compared to the jacks marked FX on my pre?

FX loop: ISP Decimator and Sonic Maximizer
As far as I'm concerned, and never having tried such a thing, I'd say to try that.

Since your pre has an FX loop, the loop's output and input impedances are probably more suited for such things, but you'll most likely not break anything putting your pedals between the pre and the power amp, so try it and decide what sounds better.
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