You wish to install a certificate into the Trusted Root Certification Authorities location using PDQ Deploy.
The following command will install the <certname>.cer file into the local system's root certificate store.
certutil.exe -addstore root \\UNCpath\certname.cer
You will need to change the UNC path to the certificate file.
For PDQ Deploy with an Enterprise license, you can use a Command Step instead of the standard Install Step and paste the command. If you are running PDQ Deploy in Free mode, create a .bat file with the same command and use an Install Step (referenced in Install File field).