Create a build specification for an .rtexe (Real Time Application), deploy it and then right click and 'Set as startup VI' and it will execute automatically after the RT target reboots.
Whoops, re-read and realised that wasn't what you asked. Apologies.
Here is my attempt to redeem myself:
I think you can do this with the System Configuration palette under Measurement IO - I think you can create a system image and then deploy it to targets programmatically. There is more information here: https://decibel.ni.com/content/docs/DOC-13216
Previously I think you used the system replication tool - there's information about that here: http://www.ni.com/white-paper/3937/en/
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