It s important to understand that the DB2 engine is embedded in the operating system. Therefore any table in any place is part of the DB2 database. It is ABSOLUTELY NOT important how the file is created (e.g. SQL, RPG, CRTPF, JDBC, COBOL, C). Also, it is ABSOLUTELY NOT important if someone calls the object a file. Everything is really a database table that is in the scope of DB2. You can test that yourself by using the system catalog on the iSeries (e.g. SYSTABLES). Notice that you can find your table in that place. Also, notice that you can use any JDBC or ODBC software to access the data on the iSeries.
That having said, there are some subtle differences. First of all, the DB2 for iSeries is a 100% real DB2 application, but is missing some things from his fellows. For example, MERGE is available on Windows and Unix, but not on the iSeries. Check the IBM Information center for this.
On the iSeries you do have some other objects that can store data. Most used are the DATAAREA and the DTAQ. These objects are NOT part of the DB2 database. Something like the FIFO object on unix is not part of the database
At last but not least, you can work with DB2 the iSeries way, or the DB2 way. The iSeries way is available for guys that grew up with the AS400. For example, you use CATALOG/TABLE instead of CATALOG.TABLE. Normally you would use the DB2 way. Every tool with iSeries support that I know off, does also support the DB2 way. Choose that option and everything works like the books.