Running 86Box.exe directly

As you probably noticed, the Manager is a completely separate program that interacts with the main 86Box program (86Box.exe) to provide you some virtual machine management capabilities. This also means you can still bypass the Manager completely and start your virtual machines directly by running 86Box directly, possibly with the -P command line argument. However, if you do this and then try to start the Manager, you'll get a warning saying this is a bad idea, though you can continue at your own risk.

To provide you with some VM management features, the Manager has to keep track of which VMs are currently running - it has to keep an eye on running instances of 86Box.exe. If you start a VM from the Manager, everything is fine, because the Manager has all the necessary information to know which VM is running in which 86Box instance. But if you start 86Box directly, there's no way for the Manager to know which VM you started (or if that VM is even on the Manager's list), and this can lead to "file in use" issues and other unpredictable situations that are best avoided entirely. That's why I decided it's best to warn the user and recommend them to close any running virtual machines first.

You'll also see a warning when you have a running VM and you try to close the Manager before closing the VM. This is related to the above situation, in the sense that if you close the Manager but keep the VM running, then restart the Manager, you'll hit the same issue I described above. In this situation, you may choose to cancel, stop all running VMs before closing Manager, or close the Manager immediately.

So, long story short: if you intend to use the Manager to manage your 86Box VMs, I recommend you use only the Manager and avoid running 86Box directly. You're free to do otherwise, at your own risk of course.