The free version should work just fine for many people. It lets you operate a single virtual hard disk for encrypting/decrypting files (more on how to do that later). Upgrading to the Unlimited Personal version enables multiple virtual drives that allow you to access several encrypted folders simultaneously; it also lets you encrypt file names, not just file contents. The Business license is the same as the Unlimited Personal license, but includes a legal clause that allows you to use it in the workplace.
The first step in setting up BoxCryptor is simply figuring out how to download the right program from the BoxCryptor website. The row of gray icons at the top of the download page looks like a simple informative image, but you'll actually need to click on the icon of your operating system to snag the installation file.
Once you have it, you'll need to double-click the file to start the installation wizard, then choose Create a new BoxCryptor folder. The next screen will ask you to choose a location for the encrypted folder. The destination can be an offline local folder, but the big draw for BoxCryptor is that it works with any cloud storage service that creates a local directory on your PC, such as the desktop clients for Dropbox, Google Drive, SkyDrive or Sugar Sync. Most cloud storage services create a local directory in C:/Users/*UserName by default. After you choose the destination folder, enter a name for the BoxCryptor folder that you're creating.
Next, you'll need to choose a drive letter designation for the virtual disk. Be sure to pick one that isn't already being used. (I chose S: for SkyDrive.) Finally, create a password, and you're good to go. I strongly recommended creating a backup of your BoxCryptor configuration file when prompted, since you'll lose the ability to descramble your data if you accidentally delete the config file and don't have a spare handy.
Reboot your PC after closing the wizard to complete the installation process. The virtual drive will appear alongside your physical drives when the computer restarts.