If you use two batteries of differing voltages without regulators, the batteries will "balance" each other. IOW, the system will draw off the higher voltage pack, until that pack's voltage is the same as the lower voltage pack. When the switches are on, the higher voltage pack will try to charge the lower voltage one, although the current flow is small due to the low voltage difference. With regulators, the system will still draw off the pack that has the higher voltage regulator, but it will not allow the two packs to cross-talk.

My usual system is two equal voltage packs with two equal voltage regulators. The capacity of the packs does not matter. If not using regulators, then two packs of equal type and voltage, again capacity does not matter.

My biggest reason for using dual packs is for redundancy, although there are other benefits. But if you are using a system that supplies the receiver and servos with separate power, keep in mind that the loss of a single pack will mean the loss of the model, unless you run redundant packs on each supply.

I also do not like a lot of stuff between the batteries and the receiver, but I have never heard of a voltage regulator failure, and using redundant batteries helps reduce that risk. I do not use or recommend the "battery backer" systems out there, I have seen problems with them.