There are two ways that I am aware of, to configure serial ports. However, both methods may not do what you wish, because, if I understand you correctly, it appears that what you need to do can only be done by hardware: I mean that you need to set jumpers on the serial card, to change it's characteristics in that way, such as altering what each pin does.
If using Linux, I suggest you look at /etc/serial.conf if this file exists on your computer; OR, investigate the `setserial` command. You can read about `setserial` by looking at the man-page:
shell$ man setserial
If you are using Windows, I cannot help. Please tell us what Operating System you are using on your MINI2440 for this task, and also try to clarify what is "The bone is QT" as this part is unclear to me.
Also, if it appears that I am misunderstanding you, please try again -- take your time, you did pretty well this time!