I have a private account on Google Drive that's not associated to any of my email addresses. Only I know about it. I use a browser that deletes history on exist. I use that account for my notes regarding TTATT and some other personal things. One of the things I've done is created a list of doctrines with four other columns (in a spreadsheet):
Doctrine | Believe | Don't Believe | Undecided | Notes
I list the doctrine, then put an X in the Believe, Don't Believe or Undecided column, then I add very brief notes to it.
I have another document that is simply a rambling of various things I've come across. This document is simply a list of "things", followed by notes about those things. Notes are usually WT articles, parallel Bible verses or Greek/Hebrew meainings. This is my main "proof" document. It's currently 26 pages long.
I have other documents that are "word studies". These are a single words (or variants) and all the scriptures in the Bible that contains that word. Nothing more. This is a hugely-eye-opening thing. For example, a study on "baptism" (including baptize, baptizing, baptized, baptisms, etc.). Very eye-opening. From this simply Bible-only view, we can deduce that baptisms were not dependent on hour and hours and months and months of studying. There's a few other things that can be deduced this way.
Organizing your thoughts in some fashion is beneficial because you can go back and review it from time to time, and even add to/edit it as necessary.
This is what I've done and what works for me for now. I'm working on another document that will be more topical with a table of contents, more like a small book. I haven't touched it in awhile, but have been meaning to get back to it. It will address core doctrines with only WT references.
It takes time, but getting these things down in writing for myrself helps me to organize my own thoughts and to reason even further on things.
That's my method. Thought I'd share.