The best use of battery power
I would put the batteries in series to ensure they all drain at the same rate. In parallel, variations in the batteries used might cause one branch to try to charge the other. The other advantage is you can then feed the whole lot into a buck converter to generate a 5V output which will be able to drain the batteries down completely.

If cost is not an issue I would just use a high performance buck IC, such as those made by Linear Technologies. These have very low standby current and are extremely efficient. However a complete implementation would cost upwards of $4-5. A cheaper option would be to power your micro with a cheap linear regulator, and have it turn on a cheap buck converter whenever the servos are required. Whether you need to put another buck converter to go from 5V to 3.3V depends on how much efficiency you're trying to squeeze out of the thing and, of course, how much you can afford to spend.