I would recomend Admin Studio if you can get it. Gives you a broader range of apps to work with.
Depending on what you have to install with, the process is pretty compicated.
If you are running an MSI install, and have multiple MSI's to install with (MSI will be the file extention for the app you are wanting to install, or will be .exe as in setup.exe) you can create a basic MSI project and then add custom actions to launch the other MSI's and install them accordingly. The Steps for this are highlighted in this document:
http://www.installshield.com/aboutus/news/newsletter/NestedInstallations.doc
To do the installs with additional setup.exe's it takes a lot of tweaking. Most of which is handled by passing commands to cmd.exe and running batch files. All of this is done in the Install Execute sequence of the install, and are handled by Custom actions that you have to configure.
The silent(unattended) install is handled in a couple ways. If the app is an MSI, you can pass the /q option to it in a batch file or from the RUN line. To do this you use this syntax:
msiexec.exe location\myprogram.msi /q
If the program is a Setup.exe, check for an INI file that goes with it and try applying the /qb switch in the CMD= (commandline=) field. If there isn't an INI file, the program will ussualy not allow you to run it quiet, so you have to deal with the prompts.
To get around the prompts you can use an app that comes with Admin Studio called Repackager. The repackaging program allows you to capture the installation and create a MSI from the captured data. If you have .exe app Installs, I would suggest getting them all to .MSI and then you can have a lot more control over how you install them.
Good Luck