sound like you have it mostly right,
current your mapping aux out 5 and 6 to be both relay and servo output. To get just the relay output you will need to set SERVO13_FUNCTION and SERVO14_FUNCTION to 0 for disabled.
Then to allow the aux pins to do something other than pwm out you need to reduce the brd_pwm_count parameter to 4. ie out of a possible 6 4 will be pwm and the last 2 are now free to do relays.
In order to control the realys you need to set the rcx_option, for 5 and 6 it would be rc_5option and rc_6option to functions 34, 35 or 36 for relay 2,3, or 4. See : http://ardupilot.org/rover/docs/parameters.html#rc5-option-rc-input-option
it looks like there is no option for relay one, i guess its reserved for motor direction changing with dc motors, so you may have to adjust your settings to use relay 2 and 3.