Ewans half way there

But if you use both batts on series (28.8v) then youll have halve the available current

No - you mean you will hold the available capacity of the 2 batteries combined.

Also the more voltage you give a motor - the more current it will pull. Hence why drill motors will fry when they run at a lot higher voltage; they simple eat the current and catch fire.

Like Ewan said - best to hook the 2 batteries together in parallel, you will get longer running time out of both motors.

As for not over volting drill motors too much - a simple guideline to make sure your drill motors are safe etc- is not to go above the drill motors voltage by 3volts.
9.6v drills on 12v is fine
12v drills on 14.4v is fine
14.4v drills on 18v is JUST about fine.

Mr Stu