I believe what you are asking is if there is a way to have your VI download into RT-Series memory but not run when executed as an EXE.
The answer is yes. When you build your application, after selecting your top-level VI on the "Source Files" tab, there is a setting on the "VI Settings" tab that allows you to select if any of the VIs in the project should "Run when Opened". The default setting for this property of a VI is FALSE/Off, but when you build it into an application, the application builder turns this TRUE/On for the top-level VI in your project. From the "VI Settings" tab you can click on any VI in the list and edit the settings of your top-level VI and explicitly tell the build to not run your top-level VI when opened, and you should be all set.