Hi Vishal,
You can specify the install location directory for any file that's included in your workspace by selecting it and setting the Installer Properties within the Deployment Tool dialog (Deployed Files tab). In the case of LabVIEW code, if you have a top-level VI that calls a subVI, then the directory in which the subVI is stored is set under the LabVIEW options. This path is relative to the directory where you indicated to install the top-level VI. This means that the installer will create a new directory (with the given name) for supporting VIs for every VI that is to be installed in a different location.
If you just want an installer that will just copy all your files onto another system with the same file structure and directories and you have LabVIEW Professional, you can try creating a source distribution.
Have a great day,
Ecleamus R.