I wouldn't suggest running a channel to each voice coil. First of all, there's no point because you've only got one cone, second (and much more importantly) it can create a lot of stress on the cone and ultimately distortion because you have one cone trying to do the job of two. For example, say voice coil 1 is running off of the left channel and voice coil 2 the right. If there is a bass guitar coming through the left channel, then voice coil 1 is trying to reproduce that. That's all fine and dandy until the bass drum starts playing and is panned to the right. Then you've got voice coil 2 doing something different then voice coil 1. Now that would be all fine and dandy if we had two different cones, but we don't, we only have one, and it's connected to both voice coil 1 and 2. So if voice coil 1 is doing something different than voice coil 2 you could get them working against eachother, which is bad for the cone. The cone is what actually makes the sound, not the voice coil.
Dual voice coil subs are not made to be played on two separate channels, they are meant for flexability in wiring. Overall there really is no point in wiring subs in stereo because low frequencies are so unidirectional that it is inaudible whether it is coming from the left or right.
So, my advice to you is to find out the lowest impedence that your amp can handle while bridged. If it's 2ohms then wire it in parallel. If it's anything more than that, either wire it in series or only wire one vioce coil, run the amp in stereo (the second channel being unused) and turn the gain all the way down on the second channel.