If you choose a folder with bitexts files instead of one file, CafeTran will import all the files in the folder, just like regular TMX memories. See the menu Memory > Import > Import bitext memory...
Thanks Igor, I've added that to the wiki article.
Hans CafeTran Wiki
Currently it is not possible to import a folder containing several bitexts. I think that with the use of AlignRobot etc. it would be a great if a whole folder of bitexts could be imported.
Bitexts automatically created during the night, can be imported in the morning when the translators start there work.