what do i do with the old omeka file once I've uploaded omeka 2.0.1?

what do i do with the old omeka file once I've uploaded omeka 2.0.1?

Do you mean when you are upgrading to 2.0.1 from an earlier version? If so, after you've made a backup of your files and database, almost all of the old files should be replaced. More instructions are here.