Best practices for second hard drive on macOS
Internal or external? Which (exact model) of Mac Mini? Without that info this answert is gonna be vague.

If it is an external SSD connected via USB-C/Thunderbolt. you could do what I did, install masOS on the external and boot from it and then use migration utility to move everything to the external SSD and used the old internal drive for incidental storage and as an "emergency" boot drive.

If it is a slower interface I would benchmark your current setup. Install your OS and files on the external and benchmark it again, then decide how to configure it.

Depending on what is in your user folder in the way of files (what kind, text, graphics, video, music) and how much you use it you could keep your user folder on on the slower drive. Mostly text docs, PDFs and the like should be no problem, but if you are editing a lot of video or graphics that is I/O intensive, keep your files on the faster drive.

If you are installing a second internal drive I would pretty much do it the same way. An internal SSD would be really fast and you would get full benefit of the speed on the internal bus. I'd put everything on the SSD.