Take a look at Samples/STDIO_SERIAL.C to see how you can redirect STDIO to serial port A at a fixed baud rate.
As with the dev board, you need to jumper SMODE to VCC to boot into programming mode, or disconnect (and possibly pull to ground -- check the schematic) to boot normally. Depending on your hardware design, you could add a switch for customers to place the board into "update" mode and use RFU to install new firmware.
If you want to use port A for something other than printf() output, you can use serAopen() and related APIs, but you'll need to disable that interface if you want to run your program in with the debugger in Dynamic C.