How do I assign a user to an unassinged number? It does not show up in Unassigned USER list.

There are a number of places where numbers can go which are not in the Unassigned.  
Check first for Phone System, Numbers, Company.  If it is there, on the user record you can add the number to either Direct or Phone (as you deem appropriate).  During the add process, you can find the Existing number you want to assign.  

Ensure you setup the User Extension first, then you can assign number(s) to the user.