As to sessions and cache coordination, when editing sessions in workbench, these changes will be reflected in the saved sessions.xml file and will not appear in any project deployment xml file as they are not associated. I did discover a problem with cache synchronization selection in the sessions editor in the workbench and have filed this bug: 314555. If this is the problem you are experiencing, you can work around this by editing the sessions.xml file directly.
As for more general deployment information, this documentation may be helpful: