All the googling around hasn't found an answer for me yet... I have one of our devs that is using VSS and VS2005. Checking in works (abeit quite painfully across the 'Net) but there doesn't seem to be a way to put comments into a checkin (unless you embed it in the source file maybe?) I'll be one of the firs to admit that my knowledge of VSS is pretty slim, and if there's a "Duh" answer, would be happy to hear it :)
When you go to check in a file(s) there should be the "fast" check in option and the check in option that has the ellipses (...) next to it indicating a dialog will open. When you use this feature to check in/out a file, there is a section in the dialog that allows you to add comments.
In Visual Studio 2005 there is a "Pending Changes" view that lets you add comments to a single file or group of files to be checked in. Pending Changes can be accessed via the View menu.
You can use the View Pending Checkins... collapsible pane in visual studio. It has a toggle button that exposes a comment box.
When checking in from the VS2005 IDE you should be prompted for check-in comments. If you are not then you probably have the "Don't show Check In dialog box when checking in items" option ticked in Tools->Options->Source Control->Environment. Untick and the check-in comment dialog will display when checking in.