Hi Marshall Harrison,
Welcome to forums.
After extracting files from .xsn file,
1. When you save InfoPath form in design view Whatever the changes you have done those are automatically reflected in template.xsn.
2. Extracted files and manifest will automatically updated when you open the template.
3. No need to extract the form again each time when you open it in design mode. You have to save changes to the form.
Hope this helps you!