When I edit a RAW file in LR 4.1, open it in PS CS6 as a smart object, then edit it in PS by double-clicking, it brings up the standalone ACR RAW editor, not LR...if I make changes, are they saved automatically to the original LR RAW file that I modified? Do I need to set preferences to make that happen or to use the LR version of the RAW editor from PS?
A Smart Object with a raw image embedds the raw file into the Photoshop file. And yes, when you edit the SO it opens in ACR not LR as designed. But, once you embed the raw SO, it's not assocated with the original raw file still in LR. There's no easy way to get the SO raw and the original raw to sync up. You can save out the XMP info to the same location as the LR raw file and import those XMP files back into LR. But that's sort of a pain...exactly why are you creating a SO from the raw and doing further edits in ACR?
That's all expected behaviour. The ACR changes are saved to the raw data contained in the smart object - not back to the original raw file.
If you want to update that raw data in LR, go to the original raw file and make the edits. Then either:
1. Edit as Smart Object, sending a new file to PS with the raw edits. Open your existing TIF file in PS, and drag this new file's smart object layer into the TIF document and delete the old smart object layer. You can now discard the new file.
2. Ctrl S / Cmd S to save the edits back to the original raw file. Open your existing TIF file in PS, right click the smart object layer, choose Replace, and point to the original raw file.
There's little to choose between the two options. I prefer the first, but the second works too.
As to why I was thinking this way in terms of workflow, first of all, I had never used LR before...and my habit, perhaps in error but one that I had grown accustomed to, was to move from Bridge to PS with the SO, make PS edits, sometimes see that I could have done more back in RAW, reopened the RAW file from the SO in PS, made the tweaks and gone back into PS to finish up. I do not know the technical underpinnings but I can now imagine that if one made PS edits that in some way relied on specific pixels or pixel relationships, what I was doing was fraught with danger in certain circumstances. The johnbeardy suggestions are helpful.