Ok, this is what I could come up with (not sure what type of batteries, so I ripped a picture of a SLA :wink: ) Basically, you will have 4 sets of (2) 12 volt batteries in parallel, in which those are wired in series to give you 36 and 48 volts along the way. This will double the amp/hour and separate out the voltage you need for each controller. Technically, you could run them both at the same time this way, two wheel drive. :lol:
Now, the first problem that you've already mentioned. When running the set at 48 volts, each battery will give it's part to the electrical power and thus all run down equally for the most part. But, when you switch to the 36 volt set, those two extra 12 will basically sit there and do nothing. So all the batteries in the 36 volt set will run down before the (2) idle 12 volt batteries.
This does leave an interesting problem, basically how do you charge them all? Well in this case, you could chance a high amp @ 48 volt charger, but it just means those two extra 12 volt batteries will take a beating upon every recharge since they will not be as depleted as the rest. Another alternative would be to use two chargers, one for th 36 volt set, the other for the 12 volt set. This could work because I did this on my e-bike before because I had a mix of SLA and NiMH batteries at once point long ago.
Another alternative is to simply put the 48 volts into both controllers. I'm not sure how much that 36 volt controller can take, but a simple heat test @ 48 volts should let you know if you should try this or not. Just hook up the 48 volts and turn on the power. Put your hand on the metal fins for the heat sink and if they start to get hot, cut power immediately. It means the controller just won't take the extra power. If it passes the heat overload test @ 48 volts just sitting there, try giving the motor some power for about 15 seconds and feel that controller again. If it's too hot to touch, then it won't work at that voltage because it can't get rid of the heat fast enough. If it's still cool to the touch, then it should be safe to give it a try @ 48 volts and see how it performs. If it's like all the controllers, it probably has heat overload protection. So if it can past those two test without overheating, then using it for a while and if it's starting to overheat it will shutoff on it's own. You'll know 48 volts won't work then.
Picture diagram below, have to click to get the big one (yeah it's big, have high screen resolution ready :wink: )