I would recommend bit locker. The data on the main computer is not encrypted. The Imported Items are stored as plain files. Using whole volume encryption with bitlocker would appear seamless to AC (TPM highly recommended). I'd recommend against using TruCrypt Encryption on a program directory. It's great as a container for files, but I'm not sure I would trust it with a program directory.
Remember disk-based encryption is designed to protect against physical theft.
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