When To-Do items become "done" they remain on the date they were completed. Of course, you have to have your calendar layout setup to show them somewhere. I'm not sure what the default is, but I have my calendar layout setup so that "done" To-Do items show up in the calendar view, and "To-Do" items that aren't done show up in the To-Do list. You can set this however you like by going under the "define" menu to "define calendar layouts..."

I don't know of any specific way to track billing, although your idea seems valid. There are certain To-Do items that I will use the built in timer for to keep track of how long I've spent on a task, but I don't have billable hours, so it's never been a big concern for me.

You use the "sets" feature to turn on and off particular categories. I have a set for home, for work, for everyone else's vacation schedule etc. and of course, an "everything under the sun" set. A handy feature is that the first 10 sets in your file are assigned hot keys. You can use the <command-1> through <command-10> keys on the Mac (not sure if there's a Windows counterpart (probably alt-1 through alt-10)) to scroll through the sets. I also check the preference to show the set name in the title bar so it says "Grendel's Calendar File:Home Set". These hot keys make it easy to jump through the sets quickly.