OK, in cleaning up MovableType I learned quite a bit about how it works. Here are some important notes on:
A nonobvious thing is that is a category in a tree, say portfolio is the category and the subcategory is semiconductors, and there is nothing in portfolio, then the category software won't build an index page for portfolio. There has to be at least one live entry, so even though there are entries below, the portfolio page won't build. The solution is to always have at least one blank entry or something that is perhaps the title at at each level you want to build.
The way that category archives work is that, it assumes everything that is emitted in MTEntries and MTCategories has that category tag, so if you are in the category called Press, it looks for every entry that is just equal to "Press" but *not* the subcategories. So to emit the whole thing, you actually need to sets of MTEntries, the code looks roughly like this. I've gotten rid of all the angle brackets to prevent because it is late!
...All the code to process the entries which are just equal to "press"
....All the code that processes every sub category that is here
"PluginManager":http://www.majordojo.com/projects/PluginManager/downloads/index.php. This handy manager helps you keep control of all the addons to your movabletype system.
"MTSubCategories":http://johnzeratsky.com/archives/000609.php. We use this extensively on the site, so for instance, every person has their own blog entry with is in the category person and their position is in the sub category. So to generate code to show each, it's pretty easy to do.
"Sorting Categories":http://www.movabletweak.com/categories/sorting_categories_any_way_you.php. The way that categories come out is pretty wierd and doesn't appear to be alphabetical. Of course, there is a plug in that helps. The simplest way is to take advantage of the fact it is sorting alphabetically, but you should actually use MT-Regex from Brad Choate to do this.
"Sort_Method":http://forums.sixapart.com/lofiversion/index.php/t50954.html is the advanced way to do this where you get to write your own script and stick iit there to sort the way you want.
"MT-Collate":http://www.nonplus.net/software/mt/MTCollate.htm appears to be the final way around this. It is powerful and general.