Should i run Ubuntu Server on a different drive to the one i will be using as storage or should i put it in a partition? this will be my first time using any form of linux and dont know which one to do.
I honestly recommend keeping the Operating System (OS) on a separate drive from data. If your OS drive crashes, then you can reinstall your OS on the drive, and just remount the data drive.
Granted, your data drive could crash, while your OS drive remains fine, but this is why backups should be performed regularly.