So my VPN’s software is on the AUR but was lagging behind in versions. I manually downloaded the package and pkgbuild directly from my VPN provider and manually installed with makepkg -si <package> everything works, no problem.
So today I notice I have both the AUR package installed and the manual install, I swear I uninstalled the AUR package first but maybe I was doing too much at once and forgot? It’s possible.
So my question is, how would you proceed with this? Everything is functional at the moment with the correct versions but I would like to clean this mess up now rather than later.
Would it be a competent move to just uninstall the aur package and test or should I be more cautious?
If you didn’t have conflicts with the AUR package when installing the other one, you should be able to uninstall the former without trouble.
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I’m surprised that you say you installed the vendor package with pacman, because it is rare to find any ALPM packages on vendor sites. They usually cover .rpm and .deb only — or maybe a Snap or a FlatPak. 
Now, if the vendor did indeed supply you with an ALPM-compatible package, then that package will show up as an AUR package in e.g. Octopi — I don’t know how pamac shows it, but it might be the same. So unless you’re certain that you have two versions of the same package installed, it might just be a misrepresentation.
Still, with that all said too, if the vendor package is not an ALPM package, then it is probably installed in a different location — maybe under /opt instead of in /usr — and so you could try removing the one from the AUR. But for safety’s sake, do make a full backup first, so that you can easily roll back your system to its working state if things go wrong.
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corrected mkpkg -si for pacman.
Yes the VPN provider, torguard, keeps up to date packages for all the major distributions. Windows, Mac, .deb, .rpm, arch, 32/64bit ARM. It’s nice for once.
I will just remove it tonight if there isn’t anything that stands out as dangerous, thanks all!