It's easier to open visual studio twice for most users,  here is some extra info. 

The visual micro build and upload commands will upload the project associated to the active code editor.

The visual studio debug>start commands will upload the currently selected "startup project" (shown in bold in the solution tree)

The visual studio "build>project only" commands (menu and right click) will build the currently active code editor project

The visual studio deploy command on right click context menus will upload the selected item, deploy from top menu will do as it suggests based on menu location

Visual micro will allow serial debug for two projects in a single instance on different ports but it is not advisable because all short cut keys such as F5 will work only for the last started debug session.

Right click project, "start>new instance" will start a debug session for the selected project.

Gdb debug works like normal visual studio debug, which requires one instance per ide

Summary

So, you can easily build, deploy and use multiple serial for multiple projects in a single IDE instance, but to debug multiple projects at the same time use two or more instances.

Edited the answer, was in a rush. You might still have the same conclusion but it might be clearer now.

It's just a place for me to support the plugin.