Resolution:
You can specify the logon user at  Admin GUI -> application Configuration -> Service Instance -> Server Settings -> NT Service -> Login As and Password. If you specify the user here, after deployment, the Logon user for this service will be the local user you gave. You can export this configuration by using the appmanage and using this configuration file for later deployment. At the configuration file, you can see the NT service configuration:

Example:

<NTService>
                            <runAsNT>true</runAsNT>
                            <startupType>automatic</startupType>
                            <loginAs>.\lzg</loginAs>
                            <password>#!rdiBHcHLs3nMDl0O291hzixhZwbt+KGawIDEa6t8eW8=</password>
                        </NTService>

Another way is to manually change the .tra file created for that applications. At the .tra file, these parameters are used for the NT services install/uninstall:

ntservice.interactive=false
ntservice.binary.path.absolute=C\:/tibco/bw/5.6/bin/bwengine.exe
ntservice.starttype=automatic
ntservice.name=lzgtestrv.Untitled.Process Archive
ntservice.account=.\\lzg
ntservice.displayname=TIBCO ActiveMatrix BusinessWorks (lzgtestrv.Untitled.Process Archive)
ntservice.password=\#\!xDkGA3FBa5NiQMamhNTdpM7R/v3aVEoXUgPVbToMATc\=

You can use the wrap.exe --install and --uninstall command to install or uninstall the NT services with these parameters.