Hi,

That's a good idea we will add it to the list. 

I guess you debug with one port then open the other to view the output.

You can add the ports you need to your own tool bar easily enough. Right click the tool strip and click customize. You will find two of each port under the add-in macros. One will set the project to the port and one with open the monitor in the same way that "other serial ports" does. Add both buttons then click them to see which does what you want. (We need to make the descriptions differ in future releases)

All Visual Micro commands are macros that you can add to your own menus and tool bars however using a 2nd instance of Atmel Studio might be easier.