It depends on the fader, so best way would be that you try it before. Just connect the fadermotors with a flexible cable, so that the wires can be exchanged if necessary.
Ok, I will open the case of my MIDIbox LC in order to find out which polarity I used (documentation will be published in the next days). But it doesn’t really matter. As I wrote: you just only have to exchange the two cables to the motors if you choose the wrong polarity. In worst case - if you finished your PCB and didn’t use flexible cables - I could build an option into MIOS which allows to invert the polarity via software.
Faders: Vdd should be on the upper end, so that the analog pin receives +5V when the fader is at max position.