Here is the method I use, see if this is something that you want to set up.
I have 2 machines on my network that I primarily use for media storage and downloading
MacBook Pro running Leopard - I have 3 Seagate 1.5TB FreeAgent Desk drives connected via USB. These drives store all of my movies, TV Shows and music. The movies and tv shows are primarily in iTunes compatible mp4 or divx avi’s. The music is a mix of mp3 and aac. These drives are all shared across my network. NOTE: with the exception of a few albums and a handful of tv shows, my media was NOT purchased through iTunes, so I don’t have DRM to worry about. This may be a concern for you if your media was purchased through iTunes. If so, you will probably need to employ method 2 i note below.
Windows XP Pro system - primarily a seedbox for torrents. I have a 300GB drive that I store all my downloads to that is also shared across my network.
I run iTunes on my MacBook Pro. I have most of my TV shows and movies cataloged in it so that I can search and sync whatever I need to the AppleTV. This is primarily for my wife and daughter’s benefit. It’s much easier for them to use the built in file navigation for movies and tv shows then it is trying to explain how to use the file managers that atvflash installs. I also watch podcasts from time to time and i use iTunes to maintain those. I don’t usually keep them once they’ve been watched.
I used NitoTV to map the 1.5TB shared drives as shares. I also have the 300GB drive for “new stuff” mounted as a share also. Once the drives are mounted, they are accessible using Files, Sapphire, or NitoTV in order to view them.
I myself use XBMC since I prefer the interface over the other file managers. Mapping shares is very similar in it to NitoTV and it also has the added ability to automatically sort and download artwork and plot info for tv shows and movies.
Using this system, I don’t have to connect an external drive to the AppleTV in order to view all of my content. The downside to this method is that I have to keep all of my computers running at all times. This is not a deal breaker for me since I usually keep them running 24/7 anyway.
I’m not sure how the TimeCapsule system works since I don’t have one and don’t foresee myself getting one since I have more than enough disk space right now. If it works like a standalone NAS, then you should be able to employ the same method to view all of your media without having to sync using iTunes if you don’t choose to or have to due to DRM issues. You will want to make sure that you have everything wired if possible or if you are running wireless, use 802.11 N for speed. If you have a lot of media that was purchased from iTunes, then you can always stream it instead of syncing it. This can be accomplished by leaving iTunes running on the system that you sync to the AppleTV from. All of your available media listed in iTunes will be available to view on your AppleTV via streaming.
The only other way that I can see to do what you want is to store all of your media on your TimeCapsule and have it mounted on your Mac and import all of your media into iTunes. You will want to make sure that you have the option to have iTunes organize your files turned off and also turn off the option to copy media to your iTunes folder in your home directory. You would then have the ability to sync anything you want from iTunes to your AppleTV as long as you have the disk space available on your AppleTV (either using the internal drive or connecting an external hard drive and changing the iTunes storage to external in settings).