Hi Adam
If the application is presented via Citrix then Surface Automation is the only integration technique you can use - look on the portal, there are courses specifically for SA. If the application is a Java thick-client then you will need to install Java Access Bridge. This is a Java library similar to Win32 (red spy mode) and AA (blue spy mode), but unfortunately it is not included as part of Windows. If you look in the Releases section of the portal you can find details on JAB.
In situations where your app can only be launched from another app, you need 2 objects, one for each app. The object1 starts app1 and presses the button to launch app2. Object2 then attaches to app2 when it appears. Your BP mentor should be able to advise you on exactly how to do this.