Two Cat Ports---- How is this done?

Larry, what you are trying to do is use the 5000 +RX2 as two independent radios.  This is not an easy thing to do with PowerSDR because there is only one CAT port (interface) for the entire radio and the primary and second receiver appear as VFO-A and VFO-B on the same radio; not two radios (both being VFO-A).  With DDUtil you can set up multiple CAT enabled programs to interface with the radio.  But for what you are trying to do, you need to force CWSkimmer into thinking it is controlling VFO-B and I do not think that is possible.

I know this is of little consolation, but what you are trying to do is incredibly easy to do with any FLEX-6000 radio because the CAT interface was designed to interface with the radio in such a way that each slice receiver is treated as an independent radio.  On my 6700, I have run 4 instances of CW Skimmer on 80, 40, 20 and 15m simultaneously and all track perfectly using the SDR-Bridge interface.  I can mouse click on either the CW Skimmer waterfall or the SmartSDR panafall display and the radio tunes properly and CW Skimmer tracks properly.  SDR-Bridge also has a feature to change the transmitter to the slice that I most recently tuned, making this setup essentially a point, click and work on 4 bands without changing anything on the radio (assuming my ATU already has a memory defined for the transmit frequency).

Nothing is going to happen to the 6300, 6500, 6700 except they will continue to receive SmartSDR software updates and continue to get better,