This is how to install a normal MSI file silently:
msiexec.exe /i c:\setup.msi /QN /L*V "C:\Temp\msilog.log"
Quick explanation:
/L*V "C:\Temp\msilog.log"= verbose logging at indicated path
/QN = run completely silently
/i = run install sequence
The msiexec.exe command line is extensive with support for a variety of options. Here is another overview of the same command line interface. Here is an annotated versions (was broken, resurrected via way back machine).
It is also possible to make a batch file a lot shorter with constructs such as for loops as illustrated here for Windows Updates.
If there are check boxes that must be checked during the setup, you must find the appropriate PUBLIC PROPERTIES attached to the check box and set it at the command line like this:
msiexec.exe /i c:\setup.msi /QN /L*V "C:\Temp\msilog.log" STARTAPP=1 SHOWHELP=Yes
These properties are different in each MSI. You can find them via the verbose log file or by opening the MSI in Orca, or another appropriate tool. You must look either in the dialog control section or in the Property table for what the property name is. Try running the setup and create a verbose log file first and then search the log for messages ala "Setting property..." and then see what the property name is there. Then add this property with the value from the log file to the command line.
Also have a look at how to use transforms to customize the MSI beyond setting command line parameters: How to make better use of MSI files