There seem to be quite a number of UserVoice suggestions having to do with the way floating windows work. I'd like you to consider addressing as many of these as possible in an upcoming release soon.
The thing that bugs me most and has been a problem since the beginning of L4 is that when you float a window and then go back to your main layout and open another resource, it gets opened in your floating window instead of in one of the panels that are in your main layout. This is especially irritating when you've opened a resource in a floating panel and then put it into Reading View. You're working on reading a book, say, and you want it to fill the entire screen while you're reading it, but you also want to be able to Alt+Tab back to your Logos layout to do something else (multitasking). If you open another resource while you're "doing something else" it is particularly annoying when it opens in the same panel as the resource that's in Reading View. It doesn't happen all the time. It's unpredictable. Seems to have something to do with Logos's intelligent algorithm for figuring out what panel to open a new resource in. But it should never open a new resource into an already floating or Reading View panel. I've added a new UserVoice item for this.
Here are most of the UserVoice items that deal with floating/docking windows, layouts, and opening resources:
http://logos.uservoice.com/forums/42823-logos-bible-software-5/suggestions/5737715-open-a-new-tab-should-never-go-to-a-floating-windo
http://logos.uservoice.com/forums/42823-logos-bible-software-5/suggestions/1035553-floating-window-layouts
http://logos.uservoice.com/forums/42823-logos-bible-software-5/suggestions/510677-suggestion-please-fix-the-docking-of-floating-win
http://logos.uservoice.com/forums/42823-logos-bible-software-5/suggestions/630645-assign-panels-a-resource-type-for-opening-resource
http://logos.uservoice.com/forums/42823-logos-bible-software-5/suggestions/947711-enable-us-to-drag-a-tab-out-of-the-main-window-and
http://logos.uservoice.com/forums/42823-logos-bible-software-5/suggestions/1045785-float-in-new-window
http://logos.uservoice.com/forums/42823-logos-bible-software-5/suggestions/956761-preferences-float-all-panels-on-opening
EDIT: Also review forum threads that come up in this Google search: annoying open "floating window" site:community.logos.com