When I started with make, I copied working files to a safe place, copied from the safe place to a scratch place, tweaked the scratch, got it working, etc., etc. Managing the make file was itself part of managing the project.
Then I read and thoroughly grokked the O'Reilly book on make (which some douche stole from my desk; twenty plus years on, I am still bitter about that one... ...don't miss the Tannenbaum OS book or the Stevens networking books, but the make book, it burns, it burns....)
After that all I wrote all of my make files from scratch. Doing so made sure I understood my project, its dependencies, etc., and made sure I wasn't going to accidentally corrupt a build with some edge case from another one.
make is super straightforward once you get how it works. Sort of like git rebase, I suppose (still working on that one... :->).