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No worries. Since you just have a relay for simple control, things will be pretty easy on this side. This is one of those things where you may have to test how it works without worrying to much about the theory. You can try a couple brief "ons" to see if anything gets too hot. People are justified being a bit afraid of unprotected LI-polymer batteries, however tool batteries with their protections circuits intact are substantially smaller risk.

Here is how I would probably aproach: Start by wiring the motors is series and the batteries in parallel. I assume that the motors are typically in parallel for the 12v lead acid implementation. In series they will effectivly only see 9v each, so the performance will be much reduced. However lithium batteries have much lower internal resistance so it may not be as bad as you think. Drive around the neighborhood a bit like that and if you get ok performance, and milage, switch the motors back to parrellel and test again. I suspect this will work ok performance should be good, but things may get hot (some risk of letting the magic electronic smoke out of the motors or the relay), range might be a bit poor as well. Or everything may work just dandy, stop periodically to check for eccesive heat or burning smell.