I'm wondering if this will still work or if I would need to redo how my BOs are getting filled.
This is correct. You just program for the target database, not the web service itself.
I've read the white paper and it states that one would be able to switch dynamically between the web service and using SQL directly. How's this going to work?
It is a data access layer. It is literally one line of code. If you want to swap between SQL Server and the ES (Enterprise Server) then you will just change the DataSource to use an EnterpriseServerDataSourceItem instead of a SqlDataSourceItem.
Mainly I'm wondering if there is something I need to be doing now to make life easier if we decide to use the new web server.
Program for your target database. It is literally a 5 minute implementation problem on the backend....that's the beauty! 