It'll probably be fine either way.
Er, well... honestly, after thinking about it a bit... egg on face here... if you think about how USB connectors work there is really only one possible orientation, with the passive cable nearer the "antenna" (USB-WiFi adapter). The passive cable ends with a male "B" connector (the almost-square type), no? But the active extender cable has male and female "A" connectors (the flat rectangular type), so unless you use some nonstandard gender/type adapter it really can't go the other way.
BUT: If you did have the choice, it shouldn't matter. Whichever orientation you pick, the data flowing in one direction will arrive at its destination in better condition than data flowing in the other direction, because of the not-equal cable lengths.
Consider this case:
computer-16 ft cable-hub-5 ft cable-USB wifi adapter
(The "16 foot active cable" is really just a hub with only one port and an attached cable, so I've represented it that way. Also got rid of the arrows because everything is bidirectional)
Notice that data from computer to WiFi will arrive at the WiFi adapter just 5 feet after leaving the hub (where it's been re-transmitted). Whereas data from the WiFi, after being re-transmitted by the hub, has 16 feet of cable to get through. So it will experience 3x the attenuation, distortion, noise, etc. after the hub as will data moving in the opposite direction.
Either would probably work (assuming you could physically make the connections), but the net effect is not the same for both directions. If you want symmetric effects you have to have a symmetric setup, with equal cable lengths on both sides of the repeater.
added: Here's the "diagram" with the connector types and gender added:
computerAF-AM16 ft cable-hubAF-AM5 ft cableBM-BFUSB wifi adapter
