You could just add the packages as part of your provisioning script. If you aren't using provisioning for some reason then perhaps consider the use of 'dependent packages'.
When you create a package you can say what other packages it depends on and if they are not already present it will install them all before installing that package. So you could create a simple package for each departmental collection of software and associate all other pieces of software as dependencies and then it will install them all before installing your stub package.
Give it a try, should do what you need. Just watch out if you are installing non-msi since a normal .exe installation will need detection set up so the process knows how to detect if the package is there or not. I find results vary on identifying via registry and prefer to use file detection.
Hope this helps,
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