If you want disk level encryption, LUKS is the standard Linux specification you'll need to look into. It works on the partition level so, assuming you can consolidate/repartition your RAID disk, you can set up a new partition that uses LUKS. After rebooting up the computer, you'll need to enter a password every time to unlock the encrypted partitions.
If you want to encrypt individual files manually, you want to look into gnupg and similar single-file encryption tools. These can be very labor intensive. Generally, you need to manually manage the encryption keys used with every file. You'll generally also need to enter a password each time you want to encrypt or decrypt a file.
If you want to have an encrypted directory on your existing partition, eCryptfs is one of many many tools you'll want to look into. eCryptfs will automatically encrypt every file in a directory with gnupg. The user's keyring and logon are used to store/manage encryption keys. There are many other tools that provide slightly different security management schemes. For example, there are tools that encrypt entire directories into one encrypted archive.
