I wouldn't be surprised if that is how it is wired, my Haulmark has both feeds going into one panel, but that panel is split in half (each 50A circuit has it's own set of breakers but they are all in one place). It would make more sense if the second 50A breaker in the main panel feeds the 30A panel. I would be tempted to contact Renegade and see if they have a wiring diagram for your coach. If not I would start tracing wires until I am sure of the layout before modifying.
I am not an electrician but I don't see why you couldn't install a 50A panel in place of the 30A, just make sure that the feed wire to the new 50A panel is large enough to handle the extra power and you are sure that is how it is wired.
Here is a link to help understand RV electrical (I have not read it all but it seems fairly informative).
Electrical Tutorial
How did you burn up the transfer switch? If there was a loose connection there (possible cause for switch failure), that might cause your breaker to trip...over current due to low voltage.