Yep sure you can. Plug each flexwatt strip into a power strip that is controlled by that tstat. I have noted that my Helix does say to use a power strip that does not have a surge protector on it since the Helix has it's own fuse system to handle power fluctuations.
Just make sure of two things....that all your flexwatt is the same stuff (3", 4" or 11") and that the total wattage (listed on the suppliers site - it is different for each type) does not exceed what the tstat can handle.
Our Helix is currently controlling two big racks and doing a fine job of it and I'm not even close to topping out yet on total wattage.