Just ordered a new tent and footprint (exped venus), recieved the footprint and this might seem like a really silly question but, which is the correct way to put it down?

I would guess at the tougher side down but then it would leave the taped/proofed side to be trodden on????

I'm currently using a polycro sheet, which is the same both sides.

If the manufacturer hasn't stated a preferred side, then you can do what you like. If you put the proofed side on the ground, it should be fine, so long as it doesn't get scuffed, in which case it will leak. If you put the fabric side on the ground, it will get damp, even though it shouldn't leak, but it'll need more of a wash to get mud off it than the smoother proofed side will.

For what it's worth, tent groundsheets usually have the proofed side uppermost.