The best solution is either write a script to do the job in the background (I.E. at midnight) or shovel it into the login script. (This scares users, and they like to turn the power on/off/on/off and scream)
your best bet is if the app is written correct for a networking environment the .msi file will do it nicely. otherwise you will have to purchase a network installer wrapper program.
My personal solution is to make a silent install and a script, the script executes on login installing another script that is run with the at command, and then installs as administrator at a later time... you need to learn and install perl on all your machines first, but it's worth it.