I wouldn’t call my workflow highly developed, but it works to keep me organized and on top of my craft.
Almost everything that I read as far as journal articles are pulled down from publisher websites as .ris files that include all citation information and usually a pdf of their publication. I have a Hazel rule set up to watch my Download folder that, after downloading the .ris file, opens Mendeley and moves the file into it. Mendeley then pulls down all citation info, etc. (Another Hazel rule then deletes that .ris file from the Download folder once it’s been in there for a day) I will often use citation manager software to read PDFs, but more often than I will open them in other apps such as Notability so I can read and write in the margins, much like you do. I may also type up some notes and thoughts in a Pages doc and save them with the citation as an attachment.
As far as reviewing materials often enough for them to stick in your memory, there’s a couple of ways to do this intentionally: if you’re an OmniFocus user, you can set a reminder to occasionally review these notes (drop an alias from the file location into the notes section of your task, if that works or simply put a copy of your notes there).
Something I’ve been doing recently (and I’m astonished with the profundity it’s having on me) is using Anki as I read things. Anki is more than a sophisticated flash card app, it can be used to put in questions about things that I’ve read, figures and facts, and keeps the details in my mind for as long as I review the cards regularly.