Well I've done it 2 ways in the past that both worked fine.
First option - if you're like most people and only use the latest version of the software, then uninstall the previous version before you install the new one. That works perfectly and keeps me from having lots of multiple versions on my computer (which gets confusing).
Second option - install the new version while the old version is still installed. At some point in the future, you can uninstall the old version. Just note that when you do this, it will remove the desktop and start menu shortcuts. It's really easy to go into C:\Program Files\Simplify3D-X.X.X and right-click on Simplify3D.exe and choose Send To > Desktop (create shortcut) if you need to get the shortcut back. The shortcuts are the only thing that uninstalling the old version will change.