Problem is the upsizing tool simply doesn't try to upsize all your Access queries. Many will have to be manually recreated. The main purpose of the upsizing tool is to deal with your data, that is, tables. For instance, all your data types should map correctly. Expect to have some problems with everything else.
Here is a small litany of problems you may encounter with queries:
1. The following queries are ignored: crosstab queries, parameterized action queries, action queries that contain nested queries,SQL pass-through queries, SQL DDL queries, union queries, queries that reference values on a form.
2. SELECT queries are upsized to VIEWS, but SELECT queries that contain an ORDER BY clause will often fail because Views don't support them.
3. Some action queries may be upsized but not work.
4. Form values used as parameters are a problem because all processing is performed on the server and SQL Server has no way of evaluating form values (can't see them). These queries often get upsized to user-defined functions.
5. The asterisk (*) no longer works as a wild card (you need '%')
6. Parameter queries are upsized to inline functions. (it appears that all parameter queries are upsized to functions).
7. Queries that contain user-defined functions are not upsized.
8. SQL Server and Access use different date ranges.
9. Access's concatenation operator is '&', SQL Server's is '+'.
That should give you a general idea of what's potentially involved in the migration. Definitely not as simple as one might hope.
Stored Procedures that you write on SQL Server (via the Designer of using SQL Server's client tools) will be available in the .adp interface.