If you put it in front of your amp, it will apply EQ to your guitar's tone. If you put it in the loop, it will apply EQ to your preamp's tone. Try experimenting to find what you're looking for. I've seen people very efficiently using EQ's on their preamp and guitar at the same time.
I've found myself using drastically different EQ settings on two Dual Rectos that are otherwise dialed the same because every amp has such a different personality and it takes the owner's time tweaking an EQ pedal to find the sweet spots. I like to play Tool riffs and similar styles a lot, so I amp up the low frequencies a tad and the mid frequencies a lot whilst leaving uppers at about the same... make a nice wave-like pattern and experiment with the size, range, and peak amplitude/end amplitudes of that wave.
Oh, and tell us what you find and how you like it, I still need to actually buy one and am considering many...