Anything you can do to get the charging current to the battery with the least possible electrical resistance is a good idea. Remember that you need to have a good ground connection, or you're not accomplishing anything. Paul is 100% correct with the positive battery wire from the R/R, and running a good ground wire to the battery from the case of the R/R is a good modification. Be sure you get the area where you connect the wire to on both ends as clean and shiny as possible. You will still have one extra connection in the ground circuit, but believe me, it's a lot better than trying to have the ground go through that aluminum/steel connection where the rear peg mounts. Mine was all gooped up with white corrosion, which did a great job at being a resistor - lessening the charge voltage to the battery. You'll notice all the newer units come with a ground wire as part of the unit. You want to run this directly to battery negative, as well as running the red wire to battery positive. If the wires aren't long enough, be sure to SOLDER the extensions on, a crimp or twisted wire connection is an invitation to join the dead battery club.
