I can’t say all of my notes are organized, but it is something I am working on. I use a computer program and every now and then, print out family group sheets. I am, probably unnecessarily, worried about just having the information on my computer. My sister had a computer crash and even the backup of her information would not load back in - what she printed was all she had. I put my family group sheets in sleeves in binders. When I find something new, I can just add a pages to the binder.
I have a lot of random papers from when I first started researching. To avoid adding to the pile, now I put all notes into my program - some labeled as “possible”. For example, I had a couple possible 1880 census that could be my gg-grandfather. I noted them, and later when I found his obit, I realized the siblings mentioned in the obit were the same as one of the possible census. Keeping this note with the person in my program (or in the binder) was much quicker than sorting though a pile of random notes. Also, it helps me not waste time looking up things I already found.
If I find something on a website, I copy and paste the link of the site into my notes with the information found. If I have a thought about a person when analyzing what I have found, I will put my initials and the word “note”. Sometimes it is even a note of what I have searched and what to look for next.
I personally don’t have an online tree, so I am not the best person to advise you regarding that, but I would think you would want to have your tree as your own. I have found many well researched, but others with errors. Someone who has an online tree would probably be able to advise you better on this.
Hope this gives you some ideas on what will work best for you.
Lisa