How would I connect in an independant battery pack for the receiver, would I connect it to the distribution board or via the mixer?
Neither. There should be a set of pins in the receiver, usually in the end slot where the servos plug, marked "Batt" or similar. That's where your separate battery harness goes. Don't use the 5v flylead from the P92 at the same time (although that would go into the same slot in the Rx).
Having mulled this one over I reckon that you have a battery problem here. Either you aren't charging them up for long enough, or they don't have the capacity you would have them hold, or there's a duff cell in one pack which is bringing down the other cells.
Discharge the packs down to 1v per cell, using a 12v car bulb and measuring the voltage across the bulb with a digital meter. STOP AS SOON AS THE READING GETS TO 7V. Recharge them at a known current and for a measured time, allowing about 140% of the maH capacity i.e. charge at 460mA for 14 hours (or pro-rata for different charge current).
You should now run the boat using one pack at a time and see if one is markedly down on the other one as regards the time to get the model down to horribly slow. Your idea of using a separate battery for this test is a good one, but if the battery is good then it should hold at least the 5.5v required to keep the BEC going.
FLJ