If I am running two amps from one head unit's pre-out, by connecting the second amp to the RCA outputs of the first one, do the gain controls on the first amp affect the signal sent to the second one?
Depends on the amp. some Xtants have "gain" jumpers(-20dB, -10dB,..... 20dB) as well as a sensitivity pot. With these amps input gain(the jumpers) does effect line output.
An easy way to check would be to disconnect the speakers from the first amp, adjust its gain and see if there is any volume change at the second amp.