My steps, of course after I've created my patchstick (creating a patchstick is really just a one-time deal):
1) Hack ATV from ATVUSB-Creator patchstick by booting ATV from patchstick. Once it's done its thing, pull the power, pull the thumbdrive and then re-power to reboot.
2) Once the new menu boots up go to Launcher/Downloads and install the latest Launcher and/or XBMC and/or Boxee.
At this point you could be done as XBMC & Boxee feature a bunch of great stuff along with built-in SMB networking (their apps only). If you want other "stuff"...then..
3) Go to Software Menu/3rd Party Plugins - from here you can install plugins like nitoTV, Sapphire and etc. It will also tell you if there's any updates out there as well if you've already installed them.
4) Then I'll install AFP or SMB (for non-XBMC/Boxee apps) or NFS, or any USB hacks, definitely Perian, and etc. These need to be done through nitoTV's Smart Installer so of course I install nitoTV first (step 3).
Note: Depending on what you install you will need to put a copy of the 10.4.9 ComboUpdate DMG and an ATV 1.0 Recovery DMG in your ATV's Documents folder. Directions on this is up on awkwardtv.org in Nito's Smart Installer wiki.
5) If you're using the USB hack and hanging a drive off the ATV, then you're done. If you're trying to connect through the network a shared drive, then you need to setup a network share in nitoTV's Network menu (directions up on his wiki).
Personally, I've just been using XBMC as it's easy to setup, has built-in networking, and the developer community seems to be alive and kicking. My 2¢.