Re-usable workflows will, in most cases lack the stuff you have access to while working on a list workflow (e.g. custom columns, specific content types made for list/lib etc.). If you have an array of sharepoint lists or libraries which are made using one particular template you cannot use one workflow with them - even if it was carried over correctly with a library. In true, that workflow is still associated with a library you saved a template.
Well, you can use that workflow but it will be a snapshot copy of a workflow when you saved your initial lib/list as a template. If it works and you are happy with the logic, then fine. Just note that every change/publish on a workflow will not cascade down to the libraries.
I cannot see any other way as creating a new workflow for each library (in my case 27 of them!) and copying and pasting the steps from your initial workflow.
You then have to update each and individual workflow with e.g. re-setting specific content types etc.
It would be nice to have one copy of a workflow, associated with multiple lists. One update would publish changes to all of them. This does not seem to be possible if you want to go deep with your workflow logic. Correct me if I'm wrong.