Recogito is a Web-based tool for annotating place references in early geospatial documents. It is a result of the ongoing Pelagios 3 research project, funded by the Andrew W. Mellon Foundation. This tutorial provides information on how to annotate in Recogito. For general guidance on what to annotate please the Google Doc describing Pelagios Principles.
And see AWOL's Roundup of Resources on Ancient Geography