To load extra serial ports check this article: WinCE Serial Ports | Toradex Developer Center, I believe you might have already gone through the mentioned article, but you did not save the added registry keys and values for that use SaveReg(Start > Programs > ColibriTools > SaveReg) and then reset your module, after that UART driver will be initiated at boot itself.
After saving the registry changes changing registry settings from UART would not be required from your application.
Thank you Rajat. No, I had missed that article. I did save my reg entries, but failed to add the TX and RX pin info on the two non-standard UARTs. So, the driver performs the IO pin configuration, that makes perfect sense.