Run multiple TECs in series or at multi-channel TEC controller?
You can have issues with current sharing when you put things in parallel. I know this is a big problem for LEDs and I presume you will have even worse problems with TECs.  You should either add series resistors to force a more even split, or use a dual channel driver.  If you have a good, high efficiency driver, I would recommend using a dual channel driver as it will be more efficient.