To have what you have now with noticeable more performance, just install the MPPT controller on the panel frames like the PWM. Easy peasy.
If you want to squeeze every last amp out of the system, connect the charge controller inside the RV near the batteries or the disconnect solenoid depending where you plan to tie into the RV system. Connect to the RV system with a 20 amp fuse in the positive connection. Connect a 20 amp fuse to the input of the controller from the panels with a standard connector such as the Anderson plugs or I prefer the SAE plugs. Buy new larger and longer wire (old wire was sized to carry less power) to run to the panels with the appropriate panel connections. All this, and you may reap the benefit of an extra half amp or so depending on the wire connected to the panels now.