Putting the MSP into the Updates folder will cause it to be applied every time setup.exe is ran. That can be a bad thing if you create unique MSPs which contain custom settings you only want applied during certain installs.
For example, if you don't always want OneNote installed you would create a "NoOneNote.MSP" with that app excluded. Keeping that MSP outside of the Updates folder allows you the choice on when that gets applied.
As previously mentioned you can just put the following into a Run Script task. (In the Run this script: text box....)
"<Path to setup.exe>" /adminfile "<Path to your .MSP>"