Not getting template in email sent from module

I have installed HTML Mail and Mail System modules and set them up with a template.. and it seems to be working fine when I send the test email-- it uses the template.

However when I send mail from my function in my module, it doesn't use the template.. it was my understanding this should happen automatically with all system emails, but how can I force it?

I have a mymodule_mail function that just does a switch on $key and fills $message based on various types of messages the system sends.

I call it using drupal_mail().. and that's sending properly, but not loading the template file.

I have no need of multiple templates or anything like that, just want emails sent by my module to use the default theme.