The upsizing wizzard will not convert queries to SQL SErver. You must convert them manually. also make sure that after upsizing the data to SQL Server you check all of your data types on your table to ensure that the proper datatypes have been used. Access sucks at doing this.
Read books on line on how to create stored procedures. In the meantime, you can create views on SQL server and link them to Access and filter them the same way on your front end. This will help you get started without too much of a headache to you and your users.
DTS does not create relationships. It only transfers date. It also does not upgrade your queries to views and stored procedures.