The answer to this question depends on which version of AWI you are using.
AWI v1: No, Automatic Workflow Integrator will place the order into one hotfolder based on the first rule the order
matches. The order is then ignored in any subsequent rules.
AWI v2: Yes. Each rule can be configured to allow subsequent rules to process. This is enabled on the first tab of the rule. You can then setup a second rule to place the file into a different folder.