This was my presumption (in terms of the best way to calculate wire size and Vdrop), but if I do things this way, where I get confused is how to figure out the Vdrop/losses for the total circuit.
Once I've calculated Vdrop for circuit 1 and Vdrop for circuit 2, how do I figure out what my overall losses are between the panel and the battery? Is it as simple as circuit 1 Vdrop% + circuit 2 Vdrop%?
To calculate loss, you should be figuring out the Wattage loss. (Voltage drop is only part of the total loss equation)
Power = Voltage*Current. (Watts Law)
Voltage=Current*Resistance (Ohms Law)
A bit of algebra and we get Line Loss in watts
Power =Current^2 * Resistance.
Notice that the current is squared. That is why high voltage is more efficient. If you double the voltage and halve the current you divide the line loss by 4!
To calculate loss between the Panels and the SCC, figure out the resistance of A+B and multiply it by current squared.
To calculate loss between the the SCC and the battery, figure out the resistance of A+B and multiply it by current squared.
However, if you have properly sized your wires, the line loss will be small compared to the loss in the SCC. Unfortunately, there is not formula for calculating the loss in the SCC. All you can do is go by what the manufacture says the efficiency is (if they say at all).