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. https://routerlogin.uno/

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. It's a bit more stable/feature rich than Web Highlights, but obviously doesn't give you the app functionality, however you can still use the bookmarklets on mobile.

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.

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. 

 Don't you love how people reply to threads like this without actually reading what they're replying to?

Anyway, this was a feature I also asked for ages and ages ago and Adam said was on the roadmap 'cause it was something he also wanted but... it never happened and has probably been forgotten about.

I've resorted to a third-party solution: Obsidian.md. It's a lot of setup to get it to useable state at the table for something like what you're wanting and some plugins don't work on the iOS version but for the most part it would give you everything you could want from a reference tool that can be used at the table for games as well. I realise it's not exactly what you're asking for but given the feature implementation cycle here is... let's be generous and say 'slow', I don't think annotation is coming any time soon. Something like Obsidian bypasses this need by incorporating everything into one easy to manage and alter application. Again, it's just a lot of work to set up but once you have, it's pretty amazing.