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Use Amazon EC2 as a backup server

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http://serverfault.com – I would like to use Amazon EC2 as an emergency backup database+web server in the event our primary host becomes unavailable. I feel like I wouldn't have trouble setting up a Windows instance, install SQL Server and get the web server up and running (would take a few hours, plus installing various libraries, our source code, etc). My question relates to pricing. If I simply "stop" the instance rather than "terminate" it, does that stop counting "instance-hours"? I would prefer not to terminate the instance and lose all that work I spent setting it up. If I must "terminate" in order to stop the (HowTos)