Hi,

Yes only one windows app can use the COM port but you have a couple of options that might work for you.

1)

The Visual Micro debugger always opens the Serial Monitor. The single line text box at the top of the monitor allows the keyboard to be used to send data to the Arduino.

Sending data disrupts break points that stop/halt. Non-stop break points (messages, charts and watch expressions) are okay. The reason being that when the arduino stops at a breakpoint visual micro waits for a serial command to let the arduino know it can continue. So at a stop/pause point, visual micro is looping and your code is not running.

2)
Alternatively you can use a different serial port for debugging if you hardware has more than one serial port. If not then, if the hardware supports software serial, you can use one or two digital pins along with the SoftwareSerial debugger property. 

With SoftwareSerial, one digital pin gives trace only debug. (no pause, no change expression values), two pins gives "full" debug..

You can read about how to configure the debugger to use a different port or digital pins in this article in the documentation section of visualmicro.com http://www.visualmicro.com/page/User-Guide.aspx?doc=Debugging-With-Different-Por...

You will probably need an usb>ftdi cable for 1) and 2) but you will only use up to two pins of the cable.