Doing anything on my Windows Server box is unbearably slow to the point of the system nearly being unusable...Looking into it I can see CPU isn't being used and there's plenty of RAM free. However SQL Server process is eating IO, is there a way of restricting how how much IO it uses just like memory?
Well, let me start by saying: guess why people PLAN the disc layout of their SQL Servers properly to have separate discs for databaes with TONS of IO ;) Yes, exactly - SQL Server eats all IO.
Depending on your version there is a ressource governor you can use (in SQL Server) to limit the ressource usage. In SQL Server 2012 that also includes not only CPU but IOPS limits.
Otherwise - if you ahve a SQL Server that demands tons of IO, maybe it is time to learn how to properly plan a server for your sql server? "The disc" likely does not cut it. Like not at all. THe DISCS - some of them SSD, which have a WONDERFULL IOPS limit that is like 100 times as high than hard discs - will really help.
For full details you are on the wrong place - this is a DBA question, there is dba.stackexchange.com where you can get more information about your best / a recommended disc layout. That said, you will need to provide a TON of more information for people to help you here.