Hii MonicaDiazT
I found useful information about all the steps needed in how to build a stan alone real time applications. ,Just in cas, you can review this document and see if you´re missing something.
http://zone.ni.com/reference/en-XX/help/370622F-01/lvrthowto/rt_building_rt_app/
Also I found this KB which describes in how to deploy an executable to your real time controller. If the executable is not running when you reboot the controller, you may need to verify some additional settings. You can review the NI-RT.ini settings and see if everything its configured correctly.
http://digital.ni.com/public.nsf/allkb/B37FA04A1CB84B6C862571A30060EF03
Hopefully this information will help you.