Nicolas,
NI does not currently have a programmatic API for setting up an ETS real-time target for a CVI Real-Time application. However, we are currently working on this and plan to have something similar to the LabVIEW Real-Time System Replication Tools.
In the meantime, you must use NI Measurement & Automation Explorer (MAX) to setup an ETS target with the CVI RT software and NI RT device drivers. You can use the LabWindows/CVI Real-Time File Copy Utility to download your RT DLL and support files to the target and to set your RT DLL as a startup DLL on the target. The RT File Copy Utility can be run from the CVI environment or as a standalone executable. The utility also has a command line interface you can use to run it silently from a script or your own application. You can find documentation for the RT File Copy Utility in the CVI environment help.
-Jeff
NI