If I have deep boxes from Bee Thinking and I add a Super Flow on top, what can I use as a roof since the Honey Flow roof only comes with the entire hive kit? Do I use the outer cover from Bee Thinking and place it on top of the Super Flow? Thanks!
A regular outer cover can work, but you’ll need to tilt it up to access the tool cover when harvesting. Or you can put a shim under the outer cover to elevate it slightly so it doesn’t hit the tool cover or knobs. Otherwise, on my own Flow hives I’ve got regular supers on TOP of my Flow super. This way the outer cover overhang doesn’t get in the way of the tool cover.
I am planning what Matt is doing too, but with a specific purpose.
This season I will have one full Flow hive, and one 8 frame Lang with a Flow super on it. I find that the lowest super often gets capped better if there is another super on top once it is about 2/3 full. My top super will be thin foundation or foundation-less medium frames (I am doing a comparison) to make comb honey. It will also serve to lift the outer cover above the flow key access point. 
What I didn’t point out is that comb honey sells well, and is often about twice the price of extracted honey in my area. Having said that, some people don’t like eating wax. So it pays to do a little of both.