To say "throw the FED manual away when you get it" is the same as to say "throw the MLB away when you get it" or any other ruleset.
When you work those games, use those rules, or don't work them! I work FED, ASA, USSSA, and a lot of other alphabet rulesets. I try to use them to the best of my ability as they are writen, not as I choose. I study those rulesets every day so that I know the different ones and know which ones to apply when I "put on the shirt". Since I don't work LL in my area anymore, I stopped taking the certification test every year and I am not up on the current ruleset for them, but for the rest, i look on it as a challenge to be current.