Hi,
1 : the frequency to setup in Ride project is the crystal frequency = 12 MHz for Primer 2. Note that this parameter is only used for Ride debug display (clocks, SPI and USART speed...)
2 : There is no problem to debug with Ride on "debug" port, and in the same time, to communicate with PC on "STM32" port. The PC is able to differenciate the two ports (devices differents).
For your problem, check that the USB frequency is well configured to 48 MHz on Primer2, that is the most met mistake (in this case, Windows says "Unknown device"). Check also how is managed the disconnect pin, which is different for Primer2 from ST sample (in this case, Window don't say anything). Take a look to "ms_hw_config.c" in the CircleOS project.
Hope that helps !