It's been a long time since I've used Multisim, so I'm not sure if NI include any kind of built-in version control with it, but if they do then I would strongly recommend using that.
If not, what you essentially need is a version control system suitable for binary files. Source control systems like git and SVN are not particularly suitable for this because they are designed for source code (text) where changes can be expressed differentially (i.e. as a diff).
If there's no built-in version control for Multisiom, I'd recommend looking into something like git-annex, which is a plugin for git that lets you version binary files without trying to treat the binary data itself as source. The how it works page provides a pretty good explanation:
The contents of annexed files are not stored in git, only the names of the files and some other metadata remain there.
The contents of the files are kept by git-annex in a distributed key/value store consisting of every clone of a given git repository. That's a fancy way to say that git-annex stores the actual file content somewhere under .git/annex/