I doubt that there is any automated charging system in a “standard” 2001 Beneteau. I think it’s more likely a separate wiring harness for the engine and related systems, and the house systems. As far as I know, my 2014 is still old fashioned memory (remember to turn it off) and separate switches. Yes, the wiring diagram for your era boat would be pretty sketchy (pun intended), but my 1990 Beneteau and my 2014 Beneteau had very similar basic wiring setups for connecting the batteries. Some of the newer boats have had decent wiring diagrams in the owners manual, but I’m currently stuck working from my iPad and don’t have access to my PDF version of the manual.
Hopefully, some of the other active Beneteau owners will contribute both specific knowledge of your era electrical system, and some diagrams which make sense. They’re also probably more knowledge and technically qualified than I am.
FYI, I added two 110 W flexible solar panels to my charging system last year, and it’s made a huge difference. During the period that would be the Great Lakes cruising season, I don’t worry at all about my house batteries, even with a refrigerator and a forced air heater.