Assuming it's Windows -- use the Task Scheduler to create a task that is triggered on the computer startup - before user logon, with full admin permissions.  This will ensure that there are no user-specific apps that are running.  The caveat here is that if you're dependent on any overclocking software like MSI afterburner or Precision X1, you need to either set up scripts that execute these apps before you start the miner, or have the apps execute from within the batch file before running the miner.  I have to execute X1 to get my 3rd fan spinning on my EVGA cards, but I have the script execute and then kill the application after a few minutes so it's not always running in the background taking up resources (X1 is a resource hog).