Thank you balihr! I will familiarize myself with the settings and flags in the _config file. Since I am mainly focused on the payment module customization for each store, I wanted to confirm that placing the payment module php files in /includes/languages/english/modules/payment/mytemplate effectively tells the multi-store module which payment module to use. Ex: if one store is using Authorize.net and another store is using First Data. Am I on the right track?

Thanks again,
Ray