The IDE will generate something sufficient for small projects, where
you are working alone, but is quite unwieldable for larger projects: I'm
constantly having to edit VS project files by hand, because it's so
complicated to do through the GUI, and I'm often frustrated because
there's no way to correctly specify the dependencies.
Makefiles have one of the worst syntaxes I've run into, and their
dependency management is really, really primitive. (Try adding some
comments to a key header, and you'll see what I mean.) Still, I've yet
to see anything else that even worked.
My recommendation would be: if you're busy learning C++, or some other
language, use the IDE. There's no point in overloading your learning
capacity, and anything you'll be doing until you've got some real
experience will not be complicated enough to push the IDE to its limits.
But expect to have to learn makefiles some time in your career; there
are just too many things for which nothing else works.