If you are using an external amp, then yes, you would run interconnects from the analog out jacks to the input of the equalizer, then interconnects from the output of the equalizer into your amplifier. If you're using the TA-100 as an integrated amp, though, I don't know if you could run the output from the equalizer back into an input of the preamp (assuming you're not using them all anyway) without either degrading the sound (by running it twice through the preamp circuitry) or possibly causing a problem like feedback or oscillation--someone more technically inclined might want to answer that.
If you use only one source, you might want to check the Thiel owners thread to see if anyone puts the equalizer between the source and the preamp. I never tried that when I owned Thiel CS3s, which also had an equalizer, but in theory it might work.