Dan, when sailing, you really need to keep an eye on the sail at all times, as you're continually adjusting it. That makes front seat operation impractical. Additionally, since your Mirage Drive acts as a daggerboard, it needs to be located near the center of lateral resistance (i.e. in the rear cockpit under the sail) or the boat would be weathervaning into the wind (uncontrollable weather helm). I recommend using the rear cockpit with ballast in the front (the further forward the less ballast you need) to keep the bow down. For other activities I also prefer the front seat.
On your furler installation, just make sure to bring the furling line out to the side st such an angle that it doesn't interfere with your pedals. Before drilling, lay it out in place to make sure all the parameters look good.