Running Windows 7:
If I maximize another window like the project window, the transport panel covers it. Is there a registry setting or a preference that I can set to make the transport panel have lower precedence than other windows?
No. The transport is always on top.
Turn it off (F2) and use the transport buttons on the toolbar?
I’m not sure how I finally got the transport panel to vanish with my 4 monitors, but when I start Cubase 8.5 as a template or take any project, and drag that project icon onto the cubase icon which will start that project, the transport panel never shows up. And the transport panel is not “behind” any of this because I can minimize Cubase and see my desktop.
I don’t have the transport functions in the toolbar.
As a matter of fact, the transport panel only show up when I use a KC for it and it’s a on/off function.
Here is how it looks and all 4 windows are maximized.
Well you can right+click on the Toolbar to show or hide the Transport Controls. I usually leave the Transport window closed because it is annoying and only open/close it with F2 to access stuff that won’t show up on the Project’s Toolbar like Tempo.
I went from 2 to 4 monitors recently after an enticing visit to Costco - ain’t it grand. 
Slightly off topic… But what graphics card are you using and what connector type (e.g. display port, hdmi)? Something I’d like to do in the future.
Mike.
That’s probably what I did. All I know is that the transport bar NEVER opens unless I want it to.
And yes, I don’t see how I could work with less than 4 monitors. A huge plus from Steinberg is having 3 separate mix consoles that can be linked or unlinked. It can provide a different perspective of problems from others using just 1 monitor. Cubase is so flexible, and that can be a double edged sword.
I have 2 video outputs from the motherboard and 2 more from G Force GT 640.
I will also add that the 4 monitors I use are the old-fashioned displays that are not as wide as the new ones. This does occasionally bring up a problem when someone has configured a VSTI to fit the new wide screen, therefore it overlaps onto my 2nd screen, but for me those times are rare.