First, why is this post in Patch Manager? I am moving it to Software Distribution.
Are you talking about the old package builder? That only works on XP and older and it no longer used at all as far as I know.
While Package Builder was available in 8.8 and prior, most poeple stopped using it five years ago or more.
Also, most applications are now commonly designed for scripted installs, so you don't need to repackage them with Package Builder.
You should probably use the regular installer when you set up a Distribution Package for each package and push them.
1. First create a .net 3.5 package and deploy that
You can deploy this as it is packaged. Just use the switches microsoft provides.
This AMS folder has four executable files, which are : AMS4OutlookSetup, O2003PIA, Setup and vstor. I do not know how to create a combined package for these four by using the builder and push it at one go.
Does the Vendor of AMS have documentation that tells you what order and how to run these?
If it is just a matter of launching these four executables in order, use a batch file distribution package.
The switches for .net Framework are /q /norestart
So, simply create a executable package and add this "/q /norestart" in the commandline window.