Yes, Podcasts loaded manually will not show up under "Podcasts". They have to be synced through the settings in the "Podcasts" tab in iTunes (for your iPod).
Note that, as I mentioned above, you can auto-sync your podcasts and still manage the rest of your content manually. The "Manually manage my music and videos" option only applies to the settings on the Music, Movies, and TV Shows tabs, so you can still set Podcasts to sync automatically and manage the rest of your content manually.
Of course, you can still only auto-sync your podcasts from one computer.