BoxCryptor Portable only stores files on the local Temp folder when double-clicking a file to open it. If you drag-and-drop a file from BoxCryptor to e.g. your USB stick, the file will be decrypted and stored on your usb stick in plaintext.
So a possible workflow could be:
1) Open BoxCryptor Portable
2) Drag-and-Drop the file from BoxCryptor Portable to your USB stick
3) Edit the new plaintext file on your USB stick
4) Drag-and-Drop the edited plaintext file from your USB stick to BoxCryptor Portable
Of course you need to make sure that the plaintext file is deleted securely from your USB stick afterwards - or you can even encrypt your whole USB stick with TrueCrypt (and have the BoxCryptor encrypted files in the encrypted TrueCrypt partition/container).
As gmgroeb pointed out, BoxCryptor is intended and optimized to be used with cloud storage providers like Dropbox or Google Drive. You can use BoxCryptor also to "only" encrypt your USB stick, but there may be other tools out there which fit better for this job (e.g. TrueCrypt or USB sticks with built-in hardware encryption).