Create a DSN on the SQL Server box using the Client Access ODBC driver.
This DSN should point to the AS400 libraries you want to use.
Add the AS400 server as a linked server to the SQL Server, using the DSN you created as the provider string, thus DSN=<YOUR DSN NAME>.
Product should be DB2
You should then be able to directly query your AS400 tables using something like this:
SELECT * FROM OPENQUERY(<your linked server name>, 'SELECT * FROM <DATABASENAME>.<LIBRARYNAME>.<TABLENAME>')