Do you want to use the existing information in the database or start again? If you want to use the existing info then check here (
http://modx.com/learn/modx-college/migrating-from-evo-to-revo/) first.
I've developed several sites in subdirectories from scratch (not migrating from Evo) and it's pretty much as described by sottwell above but I think it's actually easier.
Usually you should be able to just run setup in the subdirectory with a new database prefix and it should all go smoothly, as long as you have phpmyadmin access too - you may have to manually create a database with no tables in phpmyadmin first to select during setup depending on the server.
When the site is finished, back up the old files if you need them, and then remove them, move all files in the subdirectory to the root, update your config files/paths as described here (
http://rtfm.modx.com/revolution/2.x/administering-your-site/moving-your-site-to-a-new-server) and it should be good to go! I think the trickiest part is changing the prefix in the 'workspaces' table as described in the above url.
If you correct the paths in the new sites' config files before you move the subdirectory contents to the root there is zero downtime but I usually tell clients it might take an hour (it never has) and put an index.html file in the root with a site maintenance notice while I move in the new site.
I went through this process just last week, but actually moved a medium sized site of around 100 pages from a dev account on MODX Cloud (highly recommended - you can get your site working perfectly with no server issues at all) to a subdirectory install on the clients' server to tweak a few things, and then to the root. It all went perfectly.
I also highly recommend selling MODX Cloud as a new host to clients because all of my Cloud clients's sites run faster than MODX on other servers - although every one of my MODX sites has run faster than previous cms's.
Also don't forget to set the roots' robots.txt file to exclude the subdirectory while you're developing or you might get a whole lot of half finished pages indexed. I really like this way of developing because you can run all your tests in the final deployment environment.
[ed. note: atype last edited this post 12 years, 2 months ago.]