ITNinja

You can edit the shortcut locations in MSI using any packaging tool loke WISE, Installshield, ORCA..

MSI places shortcuts in the local user profile or all users profile based on the type of installation being performed. In an interactive installation, checking the box to specify the installation is intended for all users of a computer will dictate this placement. From the command line, you may dictate this by setting the public property ALLUSERS.
MSIEXEC.EXE /I MyPackage.msi
When no value is specified the application is installed "Per User" placing shortcuts in the current user profile.
MSIEXEC.EXE /I MyPackage.msi ALLUSERS=1
This installs shortcuts to the "All Users" profile, only administrators will be able to install the shortcuts in this way.
MSIEXEC.EXE /I MyPackage.msi ALLUSERS=2
For users, this will install the shortcut in the current user profile, for administrators, this will still install the profile for "All Users". As an administrator, if you wish to install the shortcuts in your own local profile, do not specify a value for the ALLUSERS property.
This public property is not set by default, but if you wish to dictate a consistent value for this property in the packages you create, edit the default MSI template in your MSI authoring/repackaging software.