You can use the iPad as an input on 3 OR 4, but not 3 AND 4. As you can see on the djay hardware compatibility page, the DDJ-1000 is not listed because it requires device drivers. So the only connection method you can use is a line out from the headphone jack of the iPad to one of the line inputs on the DDJ.
As the DDJ is a controller, not a player, it is not compatible with the rekordbox app.