DestinationDataProvider.JCO_USE_SAPGUI is a constant that specifies the logon property jco.client.use_sapgui. You may add this logon property to your *.jcoDestination file like every other logon parameter. Valid values are: 0 - do not start [default], 1 - start GUI, 2 - start GUI and hide (invisible)
I think the online docu (via provided link) is not correct regarding the meaning of values 1 and 2.
I suggest that you use the JavaDoc documentation that is shipped with the JCo SDK download archive.
Open ./javadoc/intro.html or directly ./javadoc/index.html
As explaiined by Markus, using remote function module ABAP4_CALL_TRANSACTION is a very uncommon approach for RFCs. Calling appropriate dedicated remote function modules that provide the needed functionality is recommended instead. Therefore I do not think that any JCo examples using ABAP4_CALL_TRANSACTION exist at least from SAP side.
In general, the difficulty is not with the technical handling in Java but to know what functionality an existing ABAP function module provides, what values to fill in for the import/changing/tables parameters and how to interpret the returned values in export/changing/tables parameters. So knowledge about the business logic.
The first thing to do for understanding a function module is to look into its function module documentation, if available (via SE37, for example). As the RFM ABAP4_CALL_TRANSACTION basically offers the ABAP language command "CALL TRANSACTION" with various additions to be executed remotely, appropriate ABAP knowledge would help most here.