There is a Java Integration check box in Application Modeller, you will need to tick that to interface with Java applications embedded in IE.
Also, as with any Java application you will need to ensure Java Access Bridge (JAB) is installed correctly and working (lots of help with that in the Java Automation Guide and on the Knowledgebase - Oracle also has Java Ferret and Java Monkey testing tools that can be used to check that JAB is installed and working correctly).
Finally, once JAB is installled and working you may need to experiment a bit to ensure you are attached to the correct IE process thread for the IE app. Play around with TabProcGrowth, Child Index, and if that does not work having a seperate object just for the embedded Java running (using Java instead of Browser mode).
We are limited by what is possible with the JAB interface created by Oracle - if you cannot get that working on a Java application or element then Surface Automation would be your only other way of interfacing with the application. That is why the Java Ferret/Monkey tools (downloadable as part of the JAB 2.0.2 package) is extreamly useful to check if your issue is JAB related rather than Blue Prism related.
