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In order to develop an application that accesses DB2 iSeries, you only need a JDBC driver (http://jt400.sourceforge.net/).
For a time, the latests versions of these drivers can only be used with Sun virtual machine. If it is a web application, it is always this way, because servlets servers use Sun virtual machine. However, in win applications, you can still use MS virtual machine.
The DBMS options should be changed as follows:
Access technology to set= JDBC
Database Name = AS library name
Server Name= servername or IP address
OS for iSeries Version: AS version
The latest supported version is V5R3.
There is not a specific requirement regarding PTFs, but it is important to be aware of IBM's recommendations. In particular, for jdbc access to DB2. Also when working with java applications installed on the AS under WebSphere or Tomcat.
Installing WAR in WebSphere 5.0
Creating a WAR for WebpSphere 6.0
How to improve a java application performance running on a AS/400?
Tip to avoid 'out of memory' in java applications - iSeries
How to call a stored procedure?