I think we're going to need more information. Can you give a detailed example?

Do you want to create a copy of the same workflow or use the same Workflow from different lists?
To create a copy of the Workflow, in other words a stand alone version running on your new site, you'll need to export it and import on the list in your new site. I have found problems with saving the list as Template and restoring, while your Workflow is copied along with your list template, you will not see it when you click on Manage workflows in Nintex Workflow, which means you cannot customize it. There are ways to get to the hidden Workflow list however but this would be a painful way to manage your list workflow. 
To use the same Workflow from different lists in different Sites you'll need to 
1. Create a custom Content Type for your list
2. Create a Re-usable Site Workflow and connect it to that Content Type
3. When you create a new site, create your list you want the workflow to run on and add the same content type to it.
4. From your list in the ribbon go to Workflow settings, add a workflow, Select your Content Type and then select your Workflow under "Select a Workflow Template", and then give it a name.