For comments, there are several possibilities.
Of course an important question is whether the supervisors/proof readers would want to or be willing to write into the LaTeX source.
If they would edit the LaTeX source code:
One method I like very much is to mark changes or comments by writing them in a certain colour, preferrably a different one for each commenter. Use the package
xcolor for that. If you put the logic into macros like
\NAMEcomment (with NAME being the name of the supervisor or proof reader), you also can easily search for it in the source.
Another possibility would be if your margins are wide enough, to use
\marginpar for comments. Note that you also can combine that with color (and of course, you also can put it in conveniently searchable macros).
If they would not like to edit LaTeX source code:
If they happen to have a version of Adobe Acrobat (the full program, not just the reader), you can also send them the generated PDF, and let them add their comments in that with Acrobat.
Of course there are also the standard options of either sending them the PDF and then them having their comments in a separate text file referring to the PDF (for that, having line numbers would be handy; the package
lineno should be useful in that case), or just have them writing their comments on a paper printout by hand.
And of course you could use different methods for different people. Say, your supervisor does not like to edit LaTeX but has Acrobat, then sendd him a single PDF. While some proof reader prefers to edit the LaTeX source, so you send him the source. And another proofreader would prefer to write his comments in a separate text file, so send him a PDF with line numbers.