If you select the correct connection in virt-manager (iirc it's called something like "libvirt (User session)") then you will see your Boxes VMs, and vice versa

If you select the correct connection in virt-manager (iirc it's called something like "libvirt (User session)") then you will see your Boxes VMs, and vice versa a VM created under that connection will appear in Boxes. Doesn't solve remote issues, but can still be useful if you want to e.g. set some advanced options for a Boxes VM.