As described in other "Reconstructed Cultist Manual" comments, they're encoded with "Vigenere Square". The "Completed Cultist Cipher" you have gotten also from the task contains the decryption keyword.
So go to any Veginere Sqare decipher page in the web (try Google or visit http://www.sagalore.com/vigenere.htm ). Enter the encrypted line from the Cultist manual (be careful, one missed or added letter and the result is unreadable), the keyword from the Completed Cultist Cipher, select "decrypt" and process. Voila.
-HSishi