That's pretty much it, although I'm a little confused when you said put the flexwatt half-way under the ten gallon. You have a 1-foot piece of Flex, and the 10 gallon is 10 inches wide so only 2 inches will be sticking out.

You can place the thermostat probe either taped directly on the flewatt (the section that is sticking out) or lay it inside under on the warm side (preferably in the warm hide or even under the substrate). The only problem with placing it inside is that your snake can move it around and it will throw off the temps if it moves the probe to a cooler location. Whatever you do, though, don't tape it to the inside as snake and tapes do not get along very well.

It probably doesn't matter if you place the probe on the 10 gallone Flex or the 20 gallon Flex, although you might find it difficult to adjust the temps to both tanks to the recommended settings. 3" Flex and 11" Flex operate with different wattages and different temps, plus the size of the tanks will also contribute to a different environment. You can play with the settings, though, and see if you can get them close.