Create a new folder for the definitions. Each new definition will be a separate document in that folder, with the title being the word or concept and the body of the document the definition itself.
In the text, when you enter a word that has already been defined, enter it in [[square brackets]] and this will create a wiki link to the definition document – if you enter the first few letters and press either cmd-escape or opt-escape (sorry, not at the mac and I can’t remember exactly), it will offer to auto-complete the title. Or you can simply select the word and choose to Add Link from the context menu – if the word is the same as one already defined, it will offer it as an auto-suggestion; otherwise you can select the desired word from the menu.
If you enter a word that needs a new definition, then simply type [[the new word]], then you will be asked where you want to create a new document (your definition folder, obviously), and a new editor or quick reference panel will open up so you can type the definition.
You’ll need to set a couple of things up first:
a) In Preferences > Corrections, make sure the wiki links box is ticked
b) In Behaviours > Document Links (I think, again I’m not at my Mac), choose how you want newly created links to open - e.g. in a quick reference panel (probably what you want), the other editor or the current editor.
I think that’s about it – there are probably a couple of wrinkles about how it works, and you should probably read the section in the manual on Document Links to get the full picture, but the above is basically how it works.
Now and then you can select the Definitions folder in the Binder and sort it alphabetically (Edit > Sort, I think, but it may be on the Documents menu!)
You can open the Definitions folder as an outline in the second editor so that you have a quick way of referring to existing definitions while you work in the main editor. Advanced tip!: use the Documents > Autocomplete > Set synopsis from text feature (approximate title…) and you’ll able to see the first part of the definitions in the outline (if you’ve set the outline to show them).
As I said, this is just one way, but it’s the way I’d choose.