Using VISA, you're a little bit limited which pins you can monitor / set. If you find you can't set /control one of the pins you want, simply make an adapter for the cable to "convert" pin 3 on your instrument side to a pin which you can control from VISA.
To control the lines, you need to open a VISA session on the required serial port, and then using the VISA property node, you can access the individual lines of the COM port. Setting them to 0 and 1 controls the signals on that line.
Hope this helps.
Shane.
Using LV 6.1 and 8.2.1 on W2k (SP4) and WXP (SP2)