If you don’t use AppV’s backend management because for example you’re using SCCM 2007, you can only manage FTA’s and shortcuts from within the package.
There is however another way, If you’re running AppV 4.6 you can add, two registry keys to manage these items on the client side. This Technet article describes the working of the two new regkeys.
If you are like me and don’t want to mess around with these registry keys, Check the downloads section for my ADM template.