I would like to set up DKIM on my domain for messages sent using Google Apps. I understand how to do this but I am concerned that if I have a DKIM DNS record for the domain, messages sent from the webserver itself (ie my website sends email in the form of password resets, order confirmations etc) they will be more likely to be treated as spam as they won't be signed in the same way as mail sent from GApps.
Have I understood this correctly and are there any implications of setting up DKIM for my domain for Google Apps?