I may have a masters degree but it definitely isn't in computer science, so this sort of thing is very difficult to grasp for me if explanations are in technical terms.
In this case it is important to understand a few fundamentals before using Bitcoin. Most important for now: if you use a paper wallet, you have to swipe the entire balance. If you only use a part, the remainder does not "stay on the paper wallet" but is transfered as change to another address. Make sure not to lose the change.
To make the transfer, you'll need a
wallet.
I was thinking of a pass phrase being like a PIN number for a debit card, an extra security needed to access an account. I didn't realize it was just a way to decode an account number.
Don't think of it as an account, think of it as a wallet. But with one crucial difference: the moment someone has seen it, he can always use it.
All of the paper wallets I've seen or used contain QR codes for each key, as well as a string of numbers beneath these keys. If these are the keys, then what is the point of encrypting something that is already in plain view on the wallet itself?
I suggest you just try it! Make a few paper wallets. Some encrypted, some not encrypted. Just see/feel/test the difference.
bitaddress.org has already been mentioned as site to create a (nice looking) paper wallet. Another option is
bitcoinpaperwallet.com.