1) Is it 'best' to sync manually or automatically?
I would go with manually, just because I distrust most things that are automatic.
2) Is there a list anywhere of problems with FTM 2012?
The closest place I know is to search this board.
3) Is there a list of problems between FTM 2012 and Ancestry.com?
4) One of the things that excited me most when I learned FTM 2012 & Ancestry could share info was the ability to import Source info from Ancestry into my FTM trees. (Census, marriages, deaths, etc..) Are there any known problems with this feature that I should be aware of? Because I'm really quite anxious to start using that feature!
This, indeed, is the neatest part of using FTM - as the gateway to the ancestry databases (NOT the trees). A couple of notes:
1) I would definitely work from FTM and let it sync up to ancestry. One prime reason for me is that Fact Notes in FTM don't sync to AMTs. I copy all kinds of stuff into Fact Notes. I use the "printer friendly" screen for copying some records directly into the Fact Notes, including Civil War Records, birth and death records - especially ones that show parents names, some census records, and many others. There are other reasons: ability to filter for where people lived, born, died, filter for different spelling variations, filter for text screens, etc, etc. Better and more expansive reports. More centralized control over things like place names.
2) Even though the access to, and automatic merging of records in ancestry datbases is the neatest thing since sliced bread (which led to the popularity of the sandwich!), the sources do have their problems. They far more wordy than they need to be, especially repeating "ancestry.com" over and over again in the same source reference note and not abbreviating words - which makes paper reports longer and longer and complicates any move they might make to the preferred way of handling footnotes on a page by page basis instead of by endnotes in paper reports (not much effect on web presentations). Also, census sources often omit the census page number - which drives me crazy.
You will quickly get hooked on using ancestry databases. The whole structure and implentatoin is very cool (except for relatively minor items noted above.)