insert document.

Is there a way a way to easily insert a document into the middle of another document? Or is cutting and pasting, then deleting the empty document the only way to go?

Yes, that’s probably the easiest way to go about it, since Merge only works on the end of the document. Something you could do that might even be easier is to Split & Merge. Just place the cursor at the insert point in the target document, and press Cmd-K—don’t bother giving it a name because it won’t exist for long. Then move the document you wish to insert in between these two parts (if they are all located around each other, you can probably do this part with the keyboard as well, using Cmd-Ctrl-ArrowKeys to move Binder elements left/right/up/down), select all three, and Merge them (Cmd-Shift-M). All of the meta-data will be used from the top document, which is what you probably want in this case.