We don’t currently have a document for this (I don’t think), but we do it all the time around here. There have been a few occasional incompatibilities or upgrade issues reported, but nothing significant that I can recall.
You should backup the db and leave it as the upgrade install option will upgrade those existing tables (thus the backup).
Next, I’d rename assets and manager folders from Etomite (e.g. assets.eto, manager.eto or similar), along with the index.php (index.php.eto) and upload the modx package into the same location. Be aware, the install packages sometimes include a subfolder in the archive /modx or /modx-0.9.x, and this can be confusing. It’s probably best to extract locally, place the contents of the /modx or /modx-0.9.x subfolder into your site root location and FTP the files, or rearchive and FTP to the server where you can extract it.
Next, take all your custom assets files from assets.eto (images, CSS files, JS files, etc.) that are used in your site design/templates, and move them back into the new MODx assets folder as appropriate (or you can do this locally before putting the files on the server).
Then, copy the /manager.eto/includes/config.inc.php file, which contains your current db settings and other important configuration information, into the same location in the new MODx manager.
Finally, go to /install/, and be sure and select the Upgrade Installation option. Please note, if the option it is not highlighted, then the system can’t find the config.inc.php file.
Other than that, everything should be pretty self-explanatory. I’ll try and get one of our talented documentation team members to expand on this and turn it into a document on the web site.
[NOTE: I was too slow posting, Ryan beat me to it, but I’m posting anyway so you can compare/contrast the approaches...]