Right then, What I need to do is pool together email addresses into a new db from multiple sources. I have some in a seperate filemaker db and some in a mysql database on my website. I have finally managed to get odbc working on my mac and have managed to access that information in a filemaker table.

How can I get the email address field from these two tables into the third with it automatically updating whenever a new one is added while not editing the data in either table?

I have tried creating relationships between them pointing towards the third table but it is not adding the emails.

You can import both tables into a third table. You can use the update matching records option. You can run this script once a day etc. You can ODBC to a FM table from MySQL but if served, you will need FMS Advanced.