I use Preview to trim textbooks. No point in having the whole thing in MarginNotes except by chapter.
If you want to use Preview to do this, make a copy of the PDF and then open it in Preview. Then you select the pages you don’t want and either just press the delete key or delete them through a menu. I usually leave the references pages in and possibly the index as well. Also leaving the table of contents in helps if you want to know that another chapter exists without having to open the PDF.
On my storage I have the text book, then a folder with the same name and “chapters” where I’ve put the extracted chapters from various textbooks I’ve done this with. I title the files with the textbook name and and ‘CHAPTER NAME ONLY’ at the end of the title. It keeps things tidy and clear.
Skimmed means I’ve used an app called Skim to make some excerpts, sometimes I use that when I don’t need to margin note overhead. I store the exported pdfd file from Skim in the folder as well. It’s transportable and can be read on any Mac with Skim.
Edit: You make a copy of the PDF because Preview automatically saves your changes and you don’t want to go deleting pages in the original textbook.