You could make a cmd that has REG ADD stuff.
CODE
start /wait %path%\Applicationsetup.exe /switches /switches
REG ADD "HKLM\Software\Microsoft\Windows\CurrentVersion\RunOnce" /v "put wateva u want here" /d "%path%\Applicationsetup2.exe /switches /switches" /f
exit
The %path% can be a variable or an absolute hardpath.
This will only work if you have to manually start the appsetup2 after reboot.
If you mean that you have switches to install it silently but after reboot, the next setup installs not-unattendedly, I can't help you.