So on SiteA, I have very simple workflows that move a document to the next "Phase" library when the document state changes from "Draft" to "Final."
I made a site template from SiteA. I used that template to create SiteB. Is there anyway I can get the URL's within my workflow to configure to the new site?
Within you workflow, if you are using reference such as Web URL or Site URL, then you dont need to change. If they are hard coded, then you need to configure them if you move to different site.
The good practice would be to use WebURL or ItemURL reference in your workflow.