T68 - Calibre and folder structure on the device

Hello,
I've been using the T68 for a month and i'm pretty satisfied with it so far.
My question is: in order to improve the speed of the search/retrieval of books from the external sd which is the best way to store the books?
Currently I have about 5000 books, they are separated in folders (per language) and in each one you can find the books as files.
The problem is that for my main languages i have more or less 12.000 files (books + metadata + covers) in the same folder, so a simple search takes a lot.
So i suspect that there would be a better way to organize them..
Any suggestions?

thank you in advance

best regards