The application builder will create an installer. Many of the driver files will be obtained automatically as well, but I think you'd have to just try it to find out. Getting dynamically loaded VI's into the application can be harder unless someone has been nice enough to place stubs for those VI's in another VI, creating a single VI to add as dynamically loaded. But, as you stated, tracking them down can be time consuming.
If you would like to keep a discussion going about how to use app builder I am willing to help. Granted, I don't know what your build deadlines like, but you can drop me a line on this thread or email me at naveen.malik@silicon-wirelss.com.
Regards,
Naveen