Hey Travis.

The reasoning behind having the upgrades in another directory is so that C5 can download everything and then switch over to the new system instantaneously (just by changing one path in a config file to point to the new core directory in "updates"). In the past there were problems where some peoples' downloads would stall or the upgrade wouldn't finish for some reason, and then their site was hosed because the old versions of the core files were half-overwritten and half-not.

If you want your core files to stay in their original location, you'll need to download the updated version of concrete5 somewhere, unzip it, and manually copy out the "concrete" directory to your current site (probably best to delete everything that's already in there first, so you don't have leftover files that were removed in the new version hanging around). If you already have the updated system in the "updates" directory, you could copy that to your top-level "concrete" directory instead of downloading a new one.

Either way, after you've done that, you'll need to remove the line in your config/site.php file that references the other directory (should be at the bottom of the config file).

Hope that helps.

-Jordan