Hey Loser,
Although a custom action will certainly allow you the flexibility to “do what you will” including installation of a cert in the cert store. I don’t think I’d advise creating one simply for that purpose. You can use the WixIISExtension and add an element to your ‘component’ requiring the certificate. This is a one liner and much less complex than using a custom action. Refer to doc here: http://wixtoolset.org/documentation/manual/v3/xsd/iis/certificate.html
In my experience creating a custom action should be a last resort as it makes debugging the installation process very difficult.