I joined rotax-owner.com and asked about the location of the fuses (or circuit breakers) for protecting the alternators and got this response from a retired electronics tech:

"You are correct that you do not want to run unfused wires long distances.  An InLine, Weatherproof, ATO Blade Style Fuse Holder can be installed within 6 inches of the Regulator.  Remember that the Capacitor needs to be installed on the Regulator (Un-Fused) side of this Fuse.

Circuit breakers are a convenience because they can often serve double duty as a switch.  Breakers do not trip without a reason.  Do not reset a breaker without first determining the reason it tripped.  This can rarely be accomplished in flight."

I definitely won't be installing my alternator CB's (or I may just go with fuses) in my panel.