Q: Is it possible to auto-sync or manually manage by content type or does it have to be one way for everything?
– Joshua

A: The answer to this is actually a bit complicated, since iTunes groups certain content types together for synchronization purposes while other types of content are handled separately.
Specifically, Music, Movies, TV Shows, Books (both iBooks and audiobooks) and Ringtones are treated as a single content group. These can be synced automatically or managed manually, but you basically have to choose one method or the other for everything. In other words, you cannot manage your movies manually while automatically syncing your music.
Each of the other types of content—Apps, Podcasts, iTunes U, Photos and Info (Contacts/Calendars/Bookmarks/Notes)—can only be synchronized automatically and are handled independently of any other content type.
If enabled, these categories of content will continue to be synchronized automatically regardless of whether you’re managing your Music/Movies/TV Shows/etc manually or not.
Note that iTunes 10 added the ability to drag-and-drop most content types directly to an iPod, iPhone or iPad even if you’re using automatic synchronization for that content. For manually added music, a separate Manually Added Songs section will appear at the bottom of the Music settings screen for your device, showing a list of songs that have been manually added and an option to remove individual items from there.
For all other content types that support this feature—basically everything except for Photos and Info—the manually added items will simply be enabled for synchronization on the appropriate settings screen, making the drag-and-drop feature essentially just a shortcut for going to the sync settings and selecting the item(s) manually.
It’s also worth noting that this separation of content types also allows different categories of content to be synced with different computers.
Although the main media content group—Music, Movies, TV Shows, Books and Ringtones—must all be synced together from a single iTunes library (or managed manually), other types can be each individually synced from additional computers. For example, you could sync your media content from a personal home computer, sync photos from a second family computer and sync apps and info from a work PC. The breakdown of content categories and groupings is as follows:
- Music, Movies, TV Shows, Books, Ringtones—sync, manual, or none
- Apps—sync or none
- Podcasts—sync or none
- iTunes U—sync or none
- Photos—sync or none
- Info (Contacts, Calendars, Bookmarks, Notes)—sync or none
Normally disabling sync for a given category will remove all of the content in that category from your device, however the last two categories—Photos and Info—are exceptions to this; when disabling sync in these cases you will be given the option to leave the content on your device or remove it.

Also keep in mind that all of this only applies to syncing content from iTunes, as opposed to using iTunes Match for your Music or wirelessly syncing info such as calendars and contacts. Music can no longer be synced directly from an iTunes library once iTunes Match has been enabled on an iOS device, and the automatic vs manual options therefore no longer apply to music in this case.