I figured it out.
- Go to an Area Page, like Site Directory, one you just created, it doesn't matter
- Click the "Add Link to Site" link, enter the Title/URL/Owner/Division, and check "include in search results"
- Now that Site will show up in the "Site directory" (http://<servername>/_layouts/1033/SearchSettings.aspx)
Each Area page has it's own "Sites" list (aka "Site Directory")... Since we only want one "Site Directory", we're going to purge the "Sites" list on all but one Area page (we'll leave it on the Area Page called "Site Index"). It has no special value other than being a custom list of all Sites in that Area or on that Portal.