The default serial output is determined by the value of BSP_DEFAULT_IO_CHANNEL (set in <mqx_dir>\mqx\source\bsp\twrk60n512\twrk60n512.h).
* "ttyf:" OSJTAG-COM pollled mode (UART5)
* "ttyd:" TWR-SER polled mode (UART3)
The default should be ttyf. That means the data comes out of UART5 on the K60 chip, and is connected to the JM60 on the tower board (which holds the OSJTAG software). The OSJTAG software then acts as a bridge to convert it to USB data.
No jumpers have to be changed to switch between the UART's. The DB9 connector on the TWR-SER is hard wired to UART3 on the K60 board. You can look at the TWR-SER and TWR-K60N512 schematics for further details.