Hi, Halfman/bike, and welcome to the Thorn Cycling Forum!
Jim is indeed correct, the hub produces AC, so polarity is not an issue there -- either lead can be attached to either hub terminal.
As for the e-Werk's DC output, it is important. The center pin is positive. If you are using the "custom" leads included to make your own connections, then the white lead is positive and black is negative.
I know from personal experience, having just installed an e-Werk on my Extrawheel trailer, described here:
http://www.thorncycles.co.uk/forums/index.php?topic=4953.0 I also checked with my tester and can doubly confirm. This is also described on page 12 of the little booklet included with the e-Werk.
So long as you get the DC leads polarized correctly, the supplied USB connectors will also be wired correctly.
As a closing cautionary note, just as important as polarity is to check to
make sure the voltage and current are appropriate for the device you are about to plug in. If your devices have different requirements, be *sure* to check every time before plugging *anything* in to the e-Werk. I have standardized my on-tour gadgets for 5vdc @ 500mA and have set the e-Werk accordingly as a fail-safe for when I am tired and wet and stoopid at the end of the day, standing by the side of the road in a rainstorm so I won't do something dumb. The cases I've heard of where people fried their gadgets with an e-Werk were all in similar circumstances, so please be careful to make sure the dials are set correctly.
The e-Werk is really a sweet little device, and I am impressed by its design and build quality. I have the Tout Terrain The Plug2+ on my Nomad, and it also works extremely well and is integrated as a stem cap. The choice between the two is really down to preference and application and whether you need only the USB 2.0-standardized ouput of 5vdc @ 500mA for the TTTP2+ or whether you need the variable output voltage and current as supplied by the e-Werk.
I hope this helps.
Best,
Dan.