Securing a system is a quite wide topic, but you seems to focus on securing the persistent storage of sensitive data against unauthorized access. In other words, you want make it more difficult for an intruder or illojal employee with access to the database to look at pdf documents he should not look at.
One approach is, as you suggest, to encrypt the documents in the database. The important and difficult decision here is how to manage the encryption key(s). Questions you should ask yorself is:
1) How can I store the encryption keys so that the application have access to them but an intruder or illojal employee do not? You can of course not store them in the database (you didn't have to encrypt the documents at all if you could trust the database). One secure but cumbersome solution is to let a trusted employee type in the keys when you start the application and only store them in memory. Another approach is to create a special, protected subsystem that only encrypt and decrypt documents.
2) What encryption algorithm is strong enough? You should probably protect against a scenario where the attacker can copy many or all of your documents to his own system and use different techniques to crack the encryption. All algorithms are in theory breakable given enough time and hardware, so the tradeoff here is to use an algorithm and keylength that makes it virtually impossible to crack the encryption and at the same time has an acceptable processing overhead (the less processing power you need to decrypt a document, the less processing power an attacker will need to crack your encryption).
3) For how long do the documents live? Encryption schemes and keys should not live forever. You should design for a system where you change your keys at regular intervals and also change encryption algorithm when they become outdated. You must also be able to handle a situation where you discover that the encryption key is compromised. In other words, it must be easy to change the key and re-encrypt all documents with the new key.
Securing a system will of course require you to do a lot more than encrypting the documents, but protecting your persistent data is not a bad start.
Good luck