I have the Mediabay and Pool setup vertically (similar to Logic) off to the right of the screen. If I need them I just use the key commands I have set up and they always pop up the same place every time. Sometimes, if I need to, I’ll grab the right edge of the arrange window and drag it to the left edge of the Mediabay or Pool window which is super fast and easy for me.
Thats weird. The transport should always stay on top of the arrange window.
You might want to try “edit in place” (ctrl- shift- I)
Eventually Cubase will have docked/tabbed windows like Logic. All the new versions of all the other Steinberg apps have it: Wavelab, Halion, Sequel, etc… Cubendo is next.