Short answer:
The search function is your friend. Search the forum.
Long answer:
Welcome to the club. Search this forum for threads on Thermotek chillers, there's been a fair bit of discussion about them.
I'm assuming you are not running the chiller inline with a separate radiator (heatercore, whatever). If you are, the radiator is acting like a heating element, and needs to be taken out.
If this is a radiatorless loop (the TECs in the chiller have some kind of heatsink, but the actual coolant loop has no heat exchanger other than the chiller unit), your overall water temperature at zero heatload shouldn't be different from the lowest temp you can get with that chiller. If you're seeing a significant change when you shut down the pump, my guess is you need more insulation on the loop. The only thing that could be increasing your temp is heat absorbtion through insufficient insulation. Or you've got a pump that's putting out a dirty great heatload, and turning it off actually makes that much of a difference (unlikely).
Again, if the cpu coolant loop has no heat exchanger other than the chiller, time spent in the chiller shouldn't matter. It's just like a radiator. Time spent in the unit only matters if it's inline with a radiator. The only gain you'll see from making a separate loop for the chiller is reduced headloss (may or may not be balanced out by the increased heatload from a second pump).
Also, bear in mind that chiller performance degrades with heatload (opposite of radiators). As you add watts to the loop, the system deals with those watts less effectively.
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