I doubt you'll get the sound of a JCM 800......but, try cutting the 200k frequency a bit. It'll help "tighten" up the tone and make it less muddy.

The advantage of running the eq through the effects loop is that the signal has already passed through the pre-amp, which is where most of the tone comes from..your then fine tuning that tone..if your running it in front of the amp, your cutting or boosting the frequencies in the signal before it even gets to the amp, so the effect is not as noticable...