I have a lot of D&D Beyond content. One thing I struggle with is actually using it for prep. As I read through the books I frequently make highlights and jot down notes. This makes my life way easier when it's time to run the game. 

Currently I'm using a browser extension called Web Highlights, but that obviously doesn't work when I'm reading the book through the app on my iPad. 

I would absolutely love it if features were added to let us highlight, annotate, and add our own reference notes to our sources. 

You could do this with pencil/paper and printouts... if you want movable markers, use miniatures (even improvised ones -- Legos, army men, chess pieces, pennies with bits of paper taped to them, magnets if you have a magnetic board, pushpins if you have a big corkboard, etc.).

If you must do it on-screen, you could do it in Adobe Illustrator, Corel Draw, GIMP, Microsoft PowerPoint, Google Slides, Open Office Impress, Keynote, depending on what illustration or slide presentation software you have access to. Spending a little time learning one of these tools might be useful down the line (school presentations, jobs, etc.) -- there are a number of ways I might approach this depending on which tool I am using. But iteration and layers are achievable in some form in all of those.

Quote from mjones517 >>

I have a lot of D&D Beyond content. One thing I struggle with is actually using it for prep. As I read through the books I frequently make highlights and jot down notes. This makes my life way easier when it's time to run the game. 

Currently I'm using a browser extension called Web Highlights, but that obviously doesn't work when I'm reading the book through the app on my iPad. 

I would absolutely love it if features were added to let us highlight, annotate, and add our own reference notes to our sources. 

You want the hypothes.is chrome extension (there's also a safari/firefox bookmarlet). It lets you annotate web pages and even share those annotations with other people. I've used it for years and it's really handy.

Quote from douji1 >>

You could do this with pencil/paper and printouts... if you want movable markers, use miniatures (even improvised ones -- Legos, army men, chess pieces, pennies with bits of paper taped to them, magnets if you have a magnetic board, pushpins if you have a big corkboard, etc.).

If you must do it on-screen, you could do it in Adobe Illustrator, Corel Draw, GIMP, Microsoft PowerPoint, Google Slides, Open Office Impress, Keynote, depending on what illustration or slide presentation software you have access to. Spending a little time learning one of these tools might be useful down the line (school presentations, jobs, etc.) -- there are a number of ways I might approach this depending on which tool I am using. But iteration and layers are achievable in some form in all of those.

 i think that Wizards would consider you using any of these resourses to be piracy.