I just went through this same thing. As Miruna said, the workflow needs to know what documents to run on. So in your workflow you'll need to add a Find Entries activity and configure it to look at the folder that will contain the documents. You'll also want to filter the entries by Documents (If the documents are in different folders, this option won't work).

After that you want to add a For Each Entry activity that will iterate through the entries found with the Find Entries activity. You will then need to make sure that the activites that run after that are running against the For Each Entry activity rather than the starting entry.

Here's an example: