If you deploy your software with EPO you can use the "command line" field in the deployment task. You can add MSI parameters there. Likewise if you don't use EPO, you can simply add the relevant parameter to the command line of the installation. Now, what kind of parameters are we talking about? Well here are a few examples and depending on the software some of them may or may not work:
MSI property: REBOOT=ReallySuppress
MSIEXEC option: /norestart
The first one tells the MSI to not reboot but depending on the installation package and the people who made it, it might be ignored and still reboot. The second one tells the msiexec.exe to not reboot but that might be superseded as well and the third one depends on the software itself because some installers have their very own switches.
I think you mean AutoBoot, as in the EEPC feature? If so, start by telling us what version of EEPC you're using.