Charging and having your speed controller hooked up at the same time is not a problem. Most speed controllers have a disable/enable option on them that you get to by the key switch. It doesn't disconnect the speed controller from power, just puts the controller in a low power mode where it wont run the motor. If your speed controller doesn't pull much current when disabled, you can leave it hooked up for months and it will just draw on the batteries a little. My Kelly controller, when disabled pulls 20mA. It has to provide 5v to the key switch so you can enable it so that's where the 20mA is going. Decent mosfets have infinite resistance when turned off so the current draw through them should be negligible with the controller off. You should be running a watt meter inline with your speed controller and batteries anyway so you will easily be able to see how much your controller is pulling on or off.
One of these little meters will do the trick and they are small and really inexpensive. You will need to get a better shunt since the one that comes with the meter is only for 50 amps.
http://www.ebay.com/itm/131630345531?_t ... EBIDX%3AIT
This is the shunt I am currently using, but I'll need to get a bigger one. 100 amps is enough for right now, but I intend on going with a much larger motor later that will pull 160+ amps. My speed controller will handle 160 amps continuous and the rest of the electrical will do 200 amps. Once I'm running on the Zippy 35C 8000mah packs I have on order I'll probably want a bigger shunt. My system is good for 200 amps except for the fuses and the shunt. Anyway, this shunt will do it for most folks going with a small scooter EV. 100 amps is a lot! I've been running this meter for a couple of months now and I just leave it on. I have nothing turning it off and it draws a few milliamps. I can't even tell it's on all the time.
http://www.ebay.com/itm/New-100A-75mV-D ... Swq5lTqmsP
I think your motors are fighting each other to some extent. You wont double your top speed with 2 motors instead of one, but torque should be significantly better. Whatever your top speed with a single motor is, well that's about all the faster you will get with 2 motors. 2 motors will just give you more acceleration until you reach the top RPM's for the motors. Hub motors are what they are, you can't gear them so the higher torque is translated into more speed. They spin only as fast as they can spin. Anyway, get your motors in sync so they track RPM wise as closely as possible. Considering how you are using 2 different speed controllers, that's probably going to be difficult since they most likely have different mosfets, programming and have different power curves as a result. Getting the motors in sync will make the whole system more efficient too and will probably give you a higher top speed and more torque. One of the things you can do keep the controllers in sync permanently is take them apart. They have an internal clock circuit for timing everything. Disconnect the clock circuit on one controller and use the clock circuit from the other controller to run both. Look at 2 identical digital watches that are set exactly to the same time. Give them a little time and they will get out of sync. Speed controllers are like the watches. The only way to make them switch motor fields at the exact same time is to use the same clock signal for both controllers. Do the speed controllers and motors have hall sensor capability? If they do, you should definitely use it. A lot of motors don't have halls built in, but they are pretty easy to add. There are a dozen threads on here that will tell you how to add them to hub motors.
Here's the halls I am using. They are commonly supported by just about any controller out there and work well. You can add halls to just about any brushless motor there is.
http://www.ebay.com/itm/161184227133?_t ... EBIDX%3AIT
Halls get you several things over a sensor-less motor.
1. Motor position is not determined by the pulses coming from the field winding's. The speed controller always knows the motor position so it is able to get it spinning in the correct direction immediately with much less cogging. The controller always knows the position of the armature even when the motor is not spinning and as a result is able to power the field windings correctly every time. You may not notice it, but in a "hallless" motor, the controller may bump the motor backwards slightly before getting the rotation correct. This is the controller getting an initial pulse to determine proper direction. The controller has a 50-50 chance of getting it right so from a dead stop so only half the time it will it bump the motor backwards and then spin it forwards. If you always kick off from a stop, then you are giving the controller those initial pulses it needs to determine direction.
2. Halls make the motor more efficient than a "hallless motor". The speed controller since it accurately knows the armatures position will always fire the field windings at the correct time. It's kind of like top dead center on your cars engine. If you fire the spark plug while the cylinder is still on the compression side of the stroke, then the engine has to overcome the downward force of the piston to maintain rotation. This is called pre-ignition and it kills engine performance. If you fire the spark plug after top dead center, then compression is being lost in the cylinder and as a result so is efficiency and power. At top dead center is the ideal time to fire the spark plug. Compression is highest and all explosive energy created in the cylinder is used to drive the piston into the down stroke. Brushless motors work similarly. You want power applied to the correct field windings at "top dead center" for that winding.
3. You mentioned that your motors are noisy at low RPM's and then things smoothed out. That's probably cogging or the motors fighting each other. Halls in the motors and controllers that are locked in sync will probably overcome a lot of that.
It sounds like you have made some good progress on this "upgrade".
By the way, those 10C batteries are not very good. A lot of people have bought them for quad and octocopters and they will run the machine, but they tend to suffer from sagging issues (loss of or reduced battery power). That 10C rating is more like 3 or 4C and the batteries are not very good quality either so their life spans tend to be short before a cell in the pack goes south. It's not an uncommon thing that people pull the packs apart. and then rebuild them out of the good cells. It may be that your battery packs can't deliver the current you need to run at full speed so you won't really know how fast you can go using them.
I was thinking about your balance charging port using a DB9 connector. The pins don't need to handle tons of current to balance the cells and if you don't care about charging your cells in 30 minutes or less, then you can always charge at a lower current and integrate everything into a single D style connector. Use a DB15 connector from a VGA port. You now have enough pins to have balance for both batteries a single connector. For your dual 6S solution, you need 2 6S balance charge ports. That's 7 pins per balance port and a DB9 only has 9 pins. The DB15 has 15 pins so for the same amount of real estate, you get all of your balancing into a single connector. Obviously charging power will still need to be a better connector.