I've got the manual handy, here.
The C60 only accommodates 12V and 24V, for some reason. If you want to connect 48V batteries, then you can only use the C40. I dunno why.
Flux, I'm not sure about the need to run all inputs together through the same charge controller. Xantrex themselves show many CC's working in parallel, on some of their most elaborate "multiple RE source" installation diagrams. I don't have them handy, but I just remember seeing them. Something I picked up from their website once, and ought to be available, still.
Your concern, Flux, about having two CC's working against each other sounds important enough to make me wary, too. If putting two in parallel, you could make sure to install them as Xantrex specifies, with common grounds, similar cable lengths, etc. and maybe pair up identical CC's, too.