Hey
Couple of things
1.) you need to ensure the you have Active Directory Powershell extensions installed on the machine you are running this from (can be done via RSAT install)
2.) you custom script devices %username% as a variable, but this variable is now passed into the commands you are running
Below is just basic write-up but should give you the idea
param([string]$user)#Load Exchange Management Environment
PowerShell.exe -command ". 'D:\Program Files\Microsoft\Exchange Server\V14\bin\RemoteExchange.ps1'; Connect-ExchangeServer -autoSet-User $user -Manager $null
Set-Mailbox $user -HiddenFromAddressListsEnabled $true
This should allow you to achieve what your after or at least point you in the right direction