Finding a low-cost program that can edit or add notes to a PDF file can be hard. Finding one that can collate all of the changes as well seems almost impossible. However, Skim For Mac might be able to solve your dilemma, as it allows users to place marks and notes into PDF files and save all of those adjustments separately as well.
Skim For Mac allows for a variety of marking and annotations to be inserted into PDF files. This free program includes movable text boxes for notes as well as highlighting, underscoring and strike-through functions. You can even change the color of the different editing marks and the notes. Hiding the marks can be done easily and can be undone just as quickly. Notes and marks can be saved as separate text files which can be useful for editing and studying. The program also allows for text searches within the PDF file. Extra tools are available to help with reading longer PDF files, including bookmarks and reading lines. The interface is easy to use but lacks a comprehensive toolbar, so you are forced to use the drop-down menus at times.
Overall, Skim For Mac seems to be a useful tool for annotating and editing PDF files with few limitations and many options. This program would be suitable for both students and personal use with editing, noting and reading PDF files.