Yes they will all be inputs, if you have a second port you can assign pins 2-9 as inputs giving you 12 extra and you still have 1, 14, 16 and 17 available as outputs.
On my Beaver Mill and lathe I have 4 positions on the rotary switch, one for Velocity mode, one for 0.01mm step one for 0.1mm step and the last for 1mm. I have since found however I never use anything other than Velocity and 0.01mm steps so on the Bridgeport I just made the two positions available. I do all my jogging Via MPG and never use the keyboard jog buttons so have never put external jog buttons on my panel, I just find MPG so much better as you wind fast it moves fast, wind slow it moves slow, change to multistep mode and each click will move the increment selected.
You would take 5v to the common of the rotary switch.
Hood