Design EVERYTHING as if it were to fail.  In the case of SimpleDeployr, when you launch a server, be careful SSH'ing in and changing things around, because if you shut that server down, you will lose your changes.

Rather than making server changes, use SimpleDeployr's "after launch" and "after deploy" scripting functionality so that every time a server is launched, you get exactly what you want!

Store your database in it's own EC2 instance, EBS instance, or use SimpleDB and RDS.  We can help you with this - don't hesitate to give us a call or email Appoxy.