Hi ihot,
all files you store in the E: drive will be encrypted by BoxCryptor and stored in encrypted form in the folder C:\personalfolder - this folder is like the "storage area" of BoxCryptor and you should not save files to this folder directly.
You can open and save files in the E: drive just as in any drive on your computer - in the background BoxCryptor reads and writes the encrypted data from/to your folder C:\personalfolder.
You can find more information how to use BoxCryptor in our manual:
http://www.boxcryptor.com/downloads/bc_win_manual_en_11.pdf
--Robert