> Make them outputs and leave floating, and set or clear?

As long as they are not tied to circuitry, this is my most preferred option.

> Make them inputs and pull up or pull down?

This works, as long as activation of the inputs won't cause the SW any
grief.
The chip will draw more current if inputs are just left floating.

> And.... speaking of inputs, what do think is best, pull up and input as
> a clear, or pull down and input as a set?

For unused, I don't see that it matters.