Question: I just started playing Fez for the first time, and I've heard there is a secret code that can be seen throughout the game. 

I'd like to know what the codes are saying, but I'm leery of looking it up in case I can figure it out on my own. Also, I don't want to spoil things if the coded text is more of a spoiler/director's commentary sort of thing.

Can this code be learned as you make your way through the game, or is it something that has to be rigorously decoded/googled to understand? Also, is it better to leave it a mystery until the second play-through?

Thank you for not posting spoilers.

Answer: 
Yes, the code can be learned through the game. However, it is not an in game mechanism, and sentences won't be automatically translated for you.

There is a special room in the game that should help you decipher the alphabet.

Deciphering this alphabet is required if you wish to finish the game to full completion, and can be done on the first playthrough.
There are 3 codes in Fez. There is the numbers code, the letters code and a third code, which I won't say much about so that you can discover it yourself. The numbers code and the third code are required to finish the game, but the letters code (alphabet) is not, it just gives you access to some backstory. All 3 codes can be deciphered before starting a New Game+.