I'm not sure about the stomp loop on the RP1000. I would imagine it is a series loop so that it sounds best with the most types of effects.
You will notice a difference placing the EQ pre- or post-. Thinking of pre- as shaping your tone before the signal hits the amp. So if you want to thicken some single coils, lean out your humbuckers, kick in a mid-boost or scoop, you can alter the inherent sound of your pickups (or fuzz/distortion if you place it after a dirt box) at the stomp of your feet.
Post- is shaping the sound of your amp before it hits the power stage. It can give you deeper control of your tone than just the low/mid/high EQ on most amps. Both pre- and post- can be very useful depending on what you're trying to achieve.
From your description, you have your wah & distortion in the stomp loop already? If you also put your EQ in the stomp loop, it will limit your options. The wah & distortion will always be better in front of your amp, so your EQ would stuck in front too. If you decide to move the stomp loop to post-, then your wah & distortion are in your loop too. Blecccch.
So I've just been looking at a schematic of the 4CM setup for the RP1000 & I figure you have two options (if I've misinterpreted your description, disregard)
1. Leave the wah & distortion in the stomp loop and place it pre-. Put the EQ in line between the amp's fx send and the RP1000's Amp Loop Return. That way the EQ is shaping the signal right out of the RM100's preamp, before you apply reverb, delay & chorus
signal:
guitar -> RP1000 in -> stomp loop (wah/dist) -> RP amp send -> RM100 in -> RM fx send -> EQ -> RP amp return -> RP line out -> RM fx return
2. put the EQ in the stomp loop. Wah & distortion are in line before your RP input. You then have the choice of moving the EQ between pre- and post- with no impact to your other pedals which should stay out front anyway
signal:
guitar -> wah -> distortion -> RP1000 in -> stomp loop (EQ) -> RP amp send -> RM100 in -> RM fx send -> RP amp return -> RP line out -> RM fx return