The only way it will control both is if the tubs share the same conditions (ie a rack situation). The only tstats that I know of that have more than one probe and can control different heating elements at different temps are the Herpstat II and Pro.
But, you could get a lamp dimmer (Lutron 300W at Lowes comes to mind) and plug one strip into it then that into the tstat. That way, you dial in the correct temp for the other flexwatt, and then can fine tune the second strip.
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