> Here are my concerns: I would like to keep as much data, like rating, keywords, labels etc. as part of the file metadata. Where does TP store all these bits of data?
Keywords and annotations that you enter through the commands under Thumbnail in the menu are stored in ThumbsPlus' database. If you wish to transfer this information into the image files themselves, you can use Image | Batch Edit Metadata for that.
That last command can also be used to enter new data into the files' metadata.
When TP makes thumbnails, it can automatically populate some fields in its database (e.g. keywords) from metadata that's stored in the image files. See Options | Preferences | Metadata.
Additionally, if you make User Fields (additional fields in the database that can be displayed below thumbnails) that have the same name as an existing IPTC or EXIF field, thumbsplus can automatically copy the value from the image to the user field in the database when thumbnails are made (see that same options screen). You could do that, for instance, if you want to see the camera model used with each thumbnail. When the information is stored in the database, you can also use it in Search.
> After making edits with outside programs how do I save the original and the changed image?
Well, that's really up to you and the external program.
If you save your edited mage to a new filename, you'll have to thumbnail that new file manually (unless 'make thumbnails automatically' is on in Opt | Pref | Thumbnails). Or, if you overwrite the existing image file, TP will show an 'Thumbnail out-of-date indicator' (a small clock symbol) on the file's thumbnail to remind you to update it.
> I use GoodSync to keep all three external USB drives synced. Are there any issues with TP in this process?
If one is your working drive and two are just backups of that, I assume you won't ever work on the backups and you'll only want to catalog the one working drive in ThumbsPlus.
You'll generally want to have your thumbsplus database on a fast local drive, but you could store a backup copy of it on the external working drive (and your sync software will then copy it onto both backup drives).
ThumbsPlus generally identifies drives by their Volume Label (not their drive letter). This might lead to two potential issues:
1) If your sync software does NOT sync the volume labels of the drives (in other words, all three have a label of their own), and you ever have to replace the working drive by a backup, then TP may not recognize the backup as being identical to the working drive. To fix this, use an external program (eg. Explorer) to give that backup drive that same volume label that your working drive used to have. Then launch TP and it should treat the backup drive as though it was the old working drive.
2) If your sync software DOES sync the volume labels of the drives (so they all have the same volume label), TP may be unable to differentiate them when two or more are online and you access them both in TP. I'm not sure - it might also use the drive serial number to tell them apart, but it's something to keep in mind to avoid problems.
As to the question about XMP sidecar files.. I don't use these myself and it's a subject that so far has barely been documented by Cerious, so I can't really answer that. Personally, I don't ever let anyone or anything modify my raw files though, and in TP, I have set the option Opt | Pref | Metadata | "Allow creation and update of metadata in raw Digicam files" firmly OFF. :)