In my initial post, I said I was using the LDS church's online journaling system as part of my study routine. It is a decent, basic system. For the purposes of the church it is all that is needed.
There is a youtube video that describes the basics of using the system.
You can keep separate notebooks for each topic or lesson or whatever, highlight text in scriptures, articles, lessons and conference talks and you can tag each note with whatever key word, words or phrases you want.
You can choose either underlining or highlighting the selected text and you have a decent selection of colors to choose from.
You cannot mark, or highlight, anything that is not on the church's website and you cannot include embed images. And, while you can include the text of a url it is not made into a link. I also have not found a way to cross-reference a highlight.
Overall, the notebook system works well but it does not quite do everything I want. So I am still looking.