It would be nice if Carnac could be enhanced to do this in a semi-automated fashion. For example, say you have a bunch of files all in one folder. It "thinks" they're probably TV Shows (based on length and whatnot). They all have the same season number, but have different episode numbers (Carnac can already get that from the filenames), but there is no [Series] available in the filename? Well, then, with all those "clues" it would make sense to look at the parent folder's name, and assign it to [Series]. It doesn't do that now, but I suspect we will continue to see this logic improve.
A lot of my older files have a very similar file/folder naming structure. I'd guess it is very common for TV Shows if people have them organized at all, much like \music\[Artist]\[Album]\[Track #] - [Name] (or some similar variant) is certainly common for music files. It would make sense to try to handle these in Carnac where possible.
However... For your problem now:
For any files you already have in a rigid folder structure, you can use the Fill Properties from Filename tool to easily get them all tagged. That won't help you for new, incoming files. But, in my experience, this isn't always a serious limitation. You can easily parse the big, existing folder structure that you have now. Then, all you need to worry about is new stuff. I have auto-import monitor my M:\incoming and T:\recordings folders, where those new files arrive.
Those files, as they are recorded or downloaded, usually have what Carnac needs as part of the filename (and if not, it is usually easily tweaked by the existing Tag On Import capabilities). So, I import them there in those "incoming" folders, Carnac figures it out, I get the metadata from thetvdb.com, and then move them into their folder structure using the Rename, Move, and Copy tool.
It would still occasionally be very useful to be able to do a similar operation with the Tag on Import rules that you can using the existing Fill Properties from Filename tool, though, for times when you need these directory structures (and filenames) "custom parsed" on an ongoing basis. I'm working on a way to do that now in a limited fashion, with MrC's help hopefully. Keep an eye on the
How To: Tag on Import thread for more (though maybe not until after the holidays).