New robot:battery drainage advice, mechanical design improvement

Ok so I found some gear motors i had lying around. They opperate somewhere around 60-70rpm. I attached them to a new quasi-chasis structure w/4AA batteries. They worked very well so the original problems i had have been solved. However when i inserted them into the actual circuit i started experiencing some rather unusual problems (i had had no actual problems with the circuit with the other motors).
Perhaps i should first explain in alitte more detail what iam doing .
An analoginput on the arduino is connnected to a 38khz ir photoreciever module. The reciever picks up the transmitter, a homemade dual-555 (one 555 for carrier 38khz, the other for modulating the carrier). The signal is demodulated in the reciever and the modulating waveform goes into the analogpin.
Basically all the arduino is doing right now is interpretting the pulse width of the signal and writing the output accordingly. The hightime(0 - period) is mapped from 0 - 255 (pwm of one motor). The lowtime (0 - period) is mapped from 0 - 255 ( pwm of other motor). The pwm values are also written to two leds that act simply as indicators.
The first problem that im having is that one of the geared motors seems to "overpower" the other. That is to say that once i turn on the "superior" motor i am unable to switch back to the "inferior" motor. Could this be because of the motors inductance and that it is pulling current away from the other motor? This is what i thought but then i saw that the indicator leds were also biased in this way. How is this possible if the leds are a completely separate circuit from the motors. Could the problem be magnetic interference? I looked through a scope and saw a lot of interference whenevr the motors were connected.
I also noticed (from looking at the indicator leds) that the transition from one motor to another when the pot was turned slowly was not smooth. Im pretty sure that this is related to the first problem .

I may upload some pics/vids if they would be helpful.
Sorry if my questions are getting annoying. And for the wordiness of my reply.
Any ideas would be welcome.