Windows 8.1 Upgrade-Question regarding SSD setup

Hi,

So I recently bought a 3XS system with a primary OS drive being a Samsung Evo SSD and a data drive being a Seagate HDD.
Scan had already set the system up to make the most of the SSD by moving the pagefile to the HDD and moving most of the User directories (with My Documents..etc) to the HDD.

I was wondering is it safe to upgrade straight from Windows 8 to 8.1 without any of these optimisations being lost or would I have to redo them again manually afterwards?

If I have to redo them I could do with a heads up on what Scan engineers did!

Thanks,

Jag