How many total servos are you powering? You can make a power setup where the batterys power both the servos and the board, with the board somewhat proteced from voltage dips caused by the servo motor starting circuit.
I am powering 6 servos, two of which are the smaller servos used for wrist rotation and gripping. (this is the lynx L6 arm)
How would I make such a system?
I was also wondering if I could just replace the 9volt battery on the VL with a 3.6 volt or less battery. How many volts does the VL require to operate?
Don’t power servos over 6V. It will blow the electronics. 
You can drop the voltage to the servos down to ~5.7v using LM7805 voltage regulators and a diode. You might need to use more than one regulator depending on how much current the arm servos are pulling. You can run power to the servo control board from the batterys via a diode to isolate the board from the high servo starting voltage drops. Put a large capacitor after the diode to the power to the board to act as a temporary power supply to the board during the voltage drops caused by the servos. There is a simple sketch at the bottom of the below page to show this type of setup.
ok, I got the robot working with a 7.2 V battery pack. The pack is connected to the BOT boards’ VL, the VL-VS jumpers on the BOT board and SSC-32 are connected, and the BOT board’s VS is wired to the SSC-32’s VS. Will this system work permanently? I want to make sure I will not damage any circuits with too much power or something.
Servos can be used up to 7.2vdc without trouble, but micro servos are a bit sensitive to this. They can become jittery. I always use 6.0vdc for my servos, with one exception. I routinely use 7.2 vdc for the hexapod 2 using HS-422 servos. The power setup above is completely acceptable. The Vreg on the SSC-32 and bot Board are low drop out and only require a very little voltage (0.10vdc I think) above the regulated voltage to work well.
Yes, the microservos do seem a little jittery. Could I have a 4AA alkaline battery pack (6v) attached to the SSC-32’s VS, and have a 2AA alkaline battery pack (3v) attached to the BOT board’s VL, link the BOT-boards VL to the SSC-32’s VL, and remove all the VL-VS jumpers?
Is 3volts enough to run the logic on both chips?
No you need at least 5.1vdc to get 5vdc from the regulator. It’s an LM2937ES so you can get the specs to be sure of the minimum required input voltage. Most cheap regs require a ful 1 volt or more above the regulated voltage to work. This one is a Low Dropout regulator.
ok. scratch that idea then. So I will be fine running both VL and VS off of the 7.2volt battery pack then?
That all depends on how many servos you want to control on the robot. If you are going to be running more than 10, I would not depend on a single battery supply. You can always run the electronics (the VL supply) off a single 9V battery and use the heavier duty battery for the servo (VS) supply.
My preference would be to never run the servos off the same battery as the electronics.
8-Dale
Ok, I run many of my 18 servo hexapods all from one 6.0vdc 2800mAh battery, VS, VL and accessories! The only problem is after a pretty long run time the Logic regulator will no longer be able to provide a stable 5vdc and the microcontroller will brown out. The legs go limp and the robot sits down. Then the battery pack will recover a bit and the robot will get up. Then a few seconds go by abd it does it again. No big deal…
Now if you run a separate 9vdc to the VL input the robot will not do the die and come back to life routine, the robot will operate a bit longer and the servos will eventually not have enough power to hold the body up.
Those are the two scenarios, pick one. 
I cannot run the VL on a separate power source because I am only allowed 9.6 volts through a single circuit for my competition - the director said that the schematics of the BOT board are not enough to prove that the VL and VS circuits are completely independant (if they are, then the robot will be legal). So I must prove they are independant somehow, or use the single battery pack.
You mentioned something about power failure in your hexapod when you did this - I am using a Lynx L6 Arm, and do not want it to fail on me in the middle of my competition. Can you give me more details on why the robot suddenly fails, when it fails, and whether the failure damages anything?
Another option I thought of - could I connect the VL-VS jumpers, run 6.0v(from 4 AA alkaline batteries) to the BOT boards VL and the SSC-32’s VL (which would then flow to the SSC-32’s VS because the jumper is connected). Would this setup provide the logic with enough power, and prevent the servos from jerking? Please answer soon, my competition is this saturday and I must begin practicing asap.
If you want to do this, it would only be good enough for the logic supply, not the servos.
You would not have much runtime from the servos with this kind of an arrangement. You best bet if you want to run the logic (Bot Board and SSC-32) and servos from a single battery is to just get a nice 6.0V 2800 mAH battery pack from Lynxmotion and use that. The amount of runtime you get will depend on how many servos you are running and how much they are running.
8-Dale
But could you ship this battery out to me fast enough for this saturdays competition? (I live near Detroit) Would a 1000 mAH 6.0v do the job? I know it will last a shorter amount of time, but I just need the robot to work for 3 minutes.
The director said the schematic is not enough to prove the two circuits are independant! 
you have got to be kidding me! How else could you prove it? I’m at a loss as to how to help you then…
Look your robot is powered by batteries. Batteries run out of energy, you can’t prevent that, it happens. That IS the failure. I explained what happens in great detail when you have one power source and when you have two power sources. The difference in run time is minimal…
One way of proving it would be to make sure the Power supply links are removed, put a supply on the VL only, then with a multimeter, prove that there is 0 volts on both banks of Servo pin supplies.
Thats if they accept multimeters as evidence…
There is a delay in shipping. I can not gaurantee you would receive them in time. Your local hobby shop could help. Yes that should be sufficient assuming it’s a new NiMH and not an old used NiCad battery from a toy you used to play with 5 years ago. Don’t ask why I’m saying this… For trouble free operation use heavy 18 gauge wires, solder connection, don’t twist the wires. In your case I would recommend a 7.2vdc 1600mAh or better, 2800mAh NiMH pack, and just live with the jittery gripper. 
I use the 7.2V 2700 mAH pack for WALTER. He only has a very few servos, so a single battery is OK in this case. Is still get at least 5 hours or so of runtime.
8-Dale
ok, i got the robot to work with the 7.2 volt battery pack, but when I grip an object too hard, the gripper starts shaking and sounds like the gears are grinding. What is wrong, and how can I fix it?