And to you as well, Gilbert.
It's been awhile, but my 5 amp circuit breaker is between the load output of my controller and my NuVinci microprocessor. I installed it there to prevent it from over amping and failing my unreplaceable microprocessor. Rightly or wrongly, I don't fuse anything else.
I am surprised that you are moving more than 10 amps anywhere with the YAF54 alternator, if you are using about the same parts as me. I would check and make sure that you have (1) alternator to rectifier, properly wired, (2) rectifier to controller input, (3) all of your load(s) from the controller to them (i.e. NO loads connected to the controller battery output), and (4) battery controller output to battery, proper poles. Per (3) I would make sure that you aren't wiring loads to the controller battery connection, but even then, the controller should be limiting amperage.
Amperages are hard to check, but I would take the volt meter that you SHOULD already own and check voltage vs. several alternator rpms for controller input, and both controller outputs, with battery connected, and loads both connected and not connected. All 4 voltages for several rpm's. I think that will clue you in to any problems, but feel free to type in your values here if you want another head scratcher.
G'luck and I think your worst case will be easily soluble. I have remained problem free since our last exchange.
Bob D.