I did some searching, and noticed a few people were having problems with installing MovableType into the SecureCGI directory, including 500 errors, and whatnot. Well, I installed it today in the scgi-bin, and using the knowledge I had gotten from a past host that only allowed you to use securecgi, I got it working, and figured I would post how I did it right here.
You need to install it as per the directions in the MovableType install manual. And, you will, when the mt-check.cgi section comes around, have to install HTML::Template, but that's pretty straight forward. However, it's the config that you have to change a little.
First, make sure you have your static directory for the docs, images, and the stylse.css file, and make sure you point that section of the config file to it, using the path as you would when you type it into the browser. So, for mine, it's like: /resources/movabletype.
Now, further down the config, you will come to the umask section. Just uncomment (Remove the #) in front of each of those items, leaving them default. Also, down further you will come to: HTMLPerms. Change that to 0644, and remove the # from the front. That may not be necessary here, however it's an extra security measure.
Now, setting up the permissions on the CGIs are another thing you have to watch for. They must be, in order for the scgi to run it, set to 744. So set all the *.cgi's in the main mt directory to 744.
And, after all that, you should be good to go. If you have any questions, you can always private message me here...and I can help you out if you need it.