While I do like the new companion binds several things together. I find it highly annoying that you cannot put the overlays or anything really on a secondary screen, Its too much clutter on the main screen.
If you have a secondary screen for viewing reports, the assumption is you’d just view the real Web site for reports/guilds. The characters window works on a secondary screen, though, as does the uploader.
When I start the companion there is an overlay ingame I don’t seem to be able to close down while having the companion open. That is the windows that it the main issue,
You have two options: you can toggle the visibility of the overlay to off and it will stay off until you bring it back, or you can tell Overwolf in its settings that you don’t want to use in-game overlays with World of Warcraft. If you do the latter, then you can just treat the Companion like a desktop app.