When you have 2 power sources in an RC airplane going from switchs to a Y or from switchs to the receiver that is parallel circuit....for the sake of this discussion we'll say the batteries are at 6 V and 4.8V right now...out put would be 5.4V. A 6V battery is 5 cell. Consider a battery discharged at 1.1V a cell and you have 5.5V .
The other thing to consider is the internal resistance of the batteries. The 4.8V battery is a load on the 6V battery...a loads by product is heat...Batteries don't like heat.
It is always best to run the same voltage and same mAh batteries in a parallel circuit where voltage stays the same but availabe current is doubled or gives longer running times between charges. Your Skyraider is probably using standard sevos, your 6V battery at say 1000mAh would be enough for all day. Heck the 4.8 battery at 700mAh would be good for 3 to 5 flights
So 2 6V 1000mAh batteries out put would be 6V, but the available current would be 2000mAh in a parallel circuit....2000mAh means that the batteries can deliver 1mA for 2000 hours or 2000 mA for 1 hour.....
Your extra battery is not needed
Good luck