voltage drop over IRF9540 = IRFZ440N H-Bridge
Without looking at your schematic I can tell you the problem- the MOSFETs are specified at 10V Vgs and you are giving them a few volts only, so they are not fully turning on. The 6V is probably dropping from the motor too. 

You need to find higher voltage drive for the gates to get them to turn on, or (easier) find MOSFETs that are specified to have low Rds(on) with a few volts Vgs. This kind of circuit should also have a UVLO (undervoltage lockout) so if the voltage is too low for them to fully turn on the MOSFETs don't get dangerously hot.