Here is a brain dump of some things I learned today about collecting code coverage information with manual tests:
Enable code coverage in the Code Coverage section of the testrunconfig options found under the Test menu similar to how you would for other tests. Because of the UI interaction requirements, manual tests are not supported via the command line mstest.exe tool. You must launch them using the IDE. The IDE will bring up a form including the instructions of the manual test and a radio button area for Pass or Fail. If you are like me you will select the radio button and then ask "How do I finish the test"? Well, above the radio button area is a somewhat nonobvious "Accept" button. Press that, and the manual test will complete. If it is the last test in the sequence, code coverage will then also finish up and present you with information in expando style so you can drill down and see how much coverage was obtained. Code coverage information should also be accessible via Team Foundation Reports although I haven't personally explored that area too much.
To publish code coverage data, the idea is that team build has published a list of builds. When you publish code coverage data you will need to select the team build the code coverage data corresponds to. Be careful here! It is all too easy to make a user mistake at this point. The dropdown menu that gives you the choices for build is actually in LRU order rather than MRU meaning the oldest build is first and the most recent build is last. You need to scroll all the way down to the bottom if you want the latest build. Also this dialog will currently allow you to associate your code coverage results with any build, so like I said, be careful. You can very easily associate code coverage results with the incorrect build.
To merge code coverage data, for example if one tester is manually working in one area and another tester is manually working in a different area - you can publish the results and associate them with the same build. And then there is an icon on the code coverage window that will allow you to merge these results together.