Can I monitor the usage of individual directories with AWS CloudWatch?

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I'm developing a platform where users will in effect have their own site within a directory of my own. Each user site will consist of a package of php scripts and the template/image files for their sites custom layout. Each user site will be connected to their own Amazon RDS. I need to be able to track the resource usage of each directory so that I can bill each user for the resources they have used. Would it be possible to setup custom metrics with CloudWatch so that I can calculate costs?

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You should be able to use cloudwatch to do this, however, it might not be the most efficient place to put this information if you are going to bill or report on it. I think you are better off computing the data and then storing it in a database of your own. This way you have easy access to the data and you can do things with data that may not work well in the context of cloudwatch.