I noticed the same issue: I have the wiring diagram. When it says 100watts x 2 channels, its splits on of those channels into the 5.25 and the 6.5. I'm looking at a way to use a second OEM FLHXSE2 amp to seperately power then, and then moving the Ipod interface to the bottom of my saddle bag.
Adding a second stock amp (when using the stock speakers) will actually decrease the output of both amps. You'll change the load from .5 ohms to 1 ohm for each amp, so the output power will drop significantly.
The reason the lowers do not sound as "full" as the fairing speakers is due to the fact that the lowers do not have a large enough enclosure to provide strong low-end. All things being equal, the fairing speakers will always sound better than the lowers.
It is possible to do it ... just not sure it makes sense to do so. You probably won't notice the drop in output wattage - it will probably play just as "loud" - but it won't change the way the speakers in the lowers "sound". IMHO, the stock SESG2/SESG3 amp is lacking at best, has proven to be COMPLETELY un-relaible (some members are on their 3rd + replaced under waranty). Maybe HD has solved the build quality issue but I am hesitant to reccommend using another stock amp (let alone the original). I've heard that the stock SESG2/SESG3 amp costs around 5 bills and for that kind of budget, there are better solutions.
Anyway ... just my thoughts ... good luck with your project and if I can help I'm more than willing to do so.