Applying mass changes to a subset of your domains only is easy:

Go to Custom Search and paste the list of domains you want to edit into the text box. If you only want to move this subset of domains to a new folder, you can already do so on this page by selecting / adding the folder in question and hitting the submit button. If you want to edit other properties of this subset of domains, simply ignore the move domain(s) to folder option and click submit.
The result page will only contain the subset of domains you pasted into the text box in step one. You can now select all these domains and edit their properties (e.g. templates, for sale sign) in bulk.

That's it!