No, it's only ONE install and ONE database. You make the modifications to that one install. During the mod installation, you'll set up a config file for each store that you want to set up. You'll also set up which stores will "see" which categories. Then just point all your stores to this ONE installation. The mod does the rest...determining which store your buyer is coming from and "feeding" them the correct template, categories, etc. Try reading the instructions with this in mind and see if it makes more sense now.
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