One persons approach:
I take a chosen defense…say the OKelly Variation of the Sicilian - 1.e4 c5, 2.Nf3 (and the alternatives) a6 from a good database or opening book, load all the main lines with branches thru about move 12. I then manually add all sorts of fairly early branches - many of which I am already familiar with because the OKelly is not very well explored in databases. I've played and researched it for years.
I then slowly tab thru each move of my database with a good engine running to display about 5 or 6 PV, adding ‘reasonable’ alternatives for my opponent not already in my new database/repertoire, but ALSO adding what might appear to be even better Black (my side) lines heretofore unexplored. In doing the latter, I can create my own 'theory' of improvements.
When that is done, I set CPT to run overnight analyzing deeper all the endpoints of the new branches I have created. This whole process helps me orient myself better and better in an opening like the OKelly. I then go back and try to identify with actual words what I as Black should try to do in these new end positions and may add a few concrete lines to CPT, noting pitfalls an unwary opponent could easily fall into. That is something I think people should look for - 'blunders' an engine spots which your opponent can fall into, and how to exploit them. It beats trying to spot them during actual game play!
In doing this, I have a GREAT feel for the defense...and have worked up a lot of good NEW ideas in the process. CPT is there to help me train them (or simply step thru the lines - as I often do - in POSITION mode)!
BTW, I have a GREAT record with the OKelly and would urge others to consider it. The really good players will NOT play 3 d4. Most below expert do which means instant equality in positions I know really well (thanks to CPT!). The best players often play 3 c4…and I steer them into lines of the Kan they would NEVER see if they met it straight away when their opponent opts for 2...e6.