Hello,
is this about Eclipse based MCU10? So yes, this is easily possible. One common way is to use the menu Window > New Window (see Go, multiply and detach: Multiple Screens with Eclipse | MCU on Eclipse): this is especially useful if you have a dual monitor system: then you can debug one project in one window while debugging the other in the other main window.
That's my preferred way.
It is possible as well to debug multiple boards/CPU's from one debug session. In that case you will have in the 'Debug' view/window the multiple cores, and you can switch between them.
The key point is that you need to tie the debug session/debug launch configuration to the correct USB Multilink: if you go into the debug settings, there is drop-down in the connection settings for P&E to select the multilink. I usually have a sticker with the USB ID on each multilink device to identify it (so I do not have to remember the number).
Hope this helps.