You've come across one of the few "price of progress" twists in the Tinderbox saga, from my own point of view.
Several major-release cycles back, probably in the Tinderbox 5 era, the program was based on a "multiple small windows" interface -- of the type you can recreate now, for instance, in Scrivener, which lets you have a main editing window and numerous "quick reference" windows on screen at the same time. For me, personally, this is the easiest and most effective way to work -- all the more so when you have a big-screen monitor. It sounds as if you have something similar in mind.
In recent years Tinderbox has switched to the "one window, many tabs" model. I understand that there were good and sufficient technical reasons for making the change. But for me, with the way I work, it was a step backward. I don't want to switch back and forth between tabs, I want to be able to see two or three of them in the same glance or perspective. To be clear: for me it was one step back, weighed against a thousand ways the program has become more convenient and powerful. (Let me tell you about the Attribute Browser ... )
There is a workaround, but it has tricks to be aware of. As @PaulWalters says, you can create multiple other windows, and get them set up the way you want. The main trick is that the window arrangement you spend time creating is not as bulletproof as you would like. In the olden days, a TB crash might zero out the multi-window layout. When you reloaded the program, you would find the data intact (I have never lost data in a TB crash or mishap) but that the XML specs for the window layout had been eliminated. Where previously you had two or three or four windows, now you had one.
That hasn't happened to me after a crash in a long time, maybe more than a year. (I believe that Mark B has changed some of the shutdown sequence for a file to minimize this risk; I'm grateful for that.) But there's another important user-induced-error possibility. Let's say you have set up three different windows for the same file. While looking at Window 3, let's say you unthinkingly hit Cmd-W, "close." That command will close Window 3 and completely eliminate its layout specs from your file, in a way that cannot be reversed by Undo or other tricks. (You might wonder how I know this.) Ie, once you have set up a multi-window arrangement, you have to be careful never to hit Cmd-W by accident, or you'll completely eliminate one of the windows and its layout.
Fortunately, there's a workaround for this. Actually two: One is to get a window layout you're happy with; then save that file; then make a copy or duplicate of the file. Then, working on the copy, you use a text editor to find the section of XML that specifies the window set-up. Then you copy that XML, and save it some place. If somehow you eliminate a window, and it would be a lot of work to re-create it, you can paste this saved XML back into your file.
The other safeguard is to use Apple's keyboard mapper, or another keyboard utility, to disable or blank-out the normal Cmd-W function within Tinderbox, so that you can't even by mistake make the deadly move. I have arranged mine so as to force an exit from any file via Shift-Cmd-W, which closes all the windows and saves their entire layout, rather than just closing and eliminating one of the windows.
For perspective: to me this is the only step backward in usability, and even so there is a way around it. Good luck.