Here's the tricky part: You can't just drag files into the BoxCryptor.bc folder that the software creates in your cloud storage directory. If you do that, the files won't be encrypted. Instead, you'll need to deposit your files directly into BoxCryptor's virtual drive--S: in my case. Doing so will also make them appear in your cloud storage folder in encrypted form.
Similarly, the only way to unencrypt your files is to withdraw them via the same virtual drive. If you try to snag your files directly through the BoxCryptor.bc folder they'll still be encrypted and you won't be able to read them.
This regimen makes accessing your files on the road a bit of a hassle, but even the free version of BoxCryptor allows users to access cloud-stored encrypted folders, assuming you have both BoxCryptor and your cloud service's desktop client installed on your PC. BoxCryptor also offers an Android app that lets you access your encrypted SkyDrive, Google Drive, and Dropbox files after you enter your BoxCryptor password. An iOS app is available, but it works only with Dropbox.
Since all the encryption and decryption action happens on BoxCryptor's virtual drive, you'll likely have no reason ever to wander into the BoxCryptor.bc folder stored in your cloud drive. If you do, however, be very, very careful not to move or delete the encfs6.xml file. That's the configuration key needed to decrypt your files. If you move or delete it, you will be unable to decrypt your files.
Maintaining multiple encrypted drives for free
Anyone who purchases BoxCryptor Unlimited has the ability to run multiple BoxCryptor virtual drives simultaneously, but free users are limited to a single virtual drive. Does that mean you can encrypt or decrypt files at only a single cloud storage service or offline location? Not at all. It simply means that you can have only a single virtual drive operating at a given time. Basically, you can create several encrypted folders, but you can encrypt or decrypt files for only one at a time.
To create another encrypted folder in a second location, right-click on the BoxCryptor icon in your system tray and select Preferences. Next, enter Advanced Mode--ignoring the warning displayed by the program--and click on the icon for your encrypted virtual disk. The Remove option will turn red and become active; click on it. Poof! Your drive disappears from the list. Don't worry, the actual files (and their encryption key) weren't deleted.