The TBM website description of that item covers the extra wires on the regulator.
The new ones have two connectors on the input and output side. It was designed to share the load since these RC connectors are good for 5A continuous. If customer wants to plug two battery packs to the input side, it is OK. But, the two packs has to be identical packs - same brand, capacity, and voltage, and in same charging status. There is NO isolation between the two packs so both packs will be drawn simultaneously. This is NOT a battery back up.
So yes, those extra wires are just that, extra. Use a zip tie to tie up the wires neatly and tuck them out of the way inside of the fuselage.
As far as charging, no you will not be able to charge through the regulator. You will need to unplug the battery and plug it directly into the charger. This is best anyway when dealing with a Lithium chemistry battery as the charge currents can be high depending on the size of the battery. You'll want to install it in the plane so that it's easy to access so you can unplug it and charge it directly. Now I know there are some that will say that it's not necessary, but I prefer to be safe and I would completely remove the battery from the plane to charge it. I place all lithium batterys such as this in a Lipo-sack when I charge them so if the battery does vent and catch fire it won't burn down my truck and my house. Also, Li-po's and Li-ions should never be left unattended when charging. But as I said, some will say they charge in the plane all the time with no problems. But to me it's not worth risking losing my plane, my car, or my house to save the couple of minutes it takes to get the battery out of the plane.
Ken