Yes, you can run your Omnisphere 3 installer if you have a previous version of Omnisphere (version 1 or 2).
Omnisphere 3 is backwards compatible. Therefore, if you have a previous version of Omnisphere installed, you can run this installer to upgrade it to Omnisphere 3. Your User data will be preserved and available in Omnisphere 3.
If you're installing with a USB, you can find instructions here:
If you're installing with the download, you can find instructions here: