I am looking into building a login system and after reading the php manual when you pass a 2 digit salt to the crypt() function it returns a hash string, and th
Yes, the salt is supposed to be kept secret, but then so is the password hash. It's perfectly acceptable for them to be kept equally secret in the same place. To check a password against the hash, you have to combine the salt with the password and then check it against the hash. So, any user or process with the right to see the password hash should also have the right to see the salt, since the password hash by itself is not useful for checking passwords (unless you're going to brute-force the salt).
The purpose of the salt is so that if two different users have the same password, they'll hash to different things. This also means that dictionary attacks are much more complex because you can't just hash all likely passwords and then check them against a list of user password hashes to find multiple user's passwords. Instead you have to try passwords for an individual salt to find one user's password or try all combinations of likely passwords with multiple salts in order to find hits. But knowledge of the salt, by itself, doesn't mean you can reverse the password hash. It just means that you can do a dictionary attack on the password hash.
If you can find a way to keep the salt more secure than the hash value, it certainly wouldn't be a bad thing, but it's hard to see how this is feasible when any program which needs access to one needs access to both.