[...] I want to use is one of these http://www.servocity.com/html/neon_fm_systems.html however it outputs two channels of square waves, and only one channel of analog wave(i think that's what it's called) which can be used to power one motor. I was wondering if there is any way I could bypass whatever circuit it is that converts the analog pot reading to a square wave, or if not what other transmitter can I use?
There's nothing to bypass. Don't buy this transmitter, it's not worth your money.
It has got only one proportional channel, the stick is probably just using one proportional channel (2 at most, but I doubt that) but it is by switches that couples different value resistors into the circuit to transmit like one proportional channel held at one out of four positions.
Same junk as cheap R/C toycars.
No intermediate speeds on such a beast (except if you use the proportional channel) and the steering is bang-bang, full left, full right or straight ahead.
One wonders why they sell such rubbish, when the production cost is about the same whether they make it fully proportional or not.