I used to have to feed little cat on top of the aquarium as fat cat would eat everything! It was more of a problem with the fat one as he was supposed to be on a balanced diet for urinary tract problems.
Don't leave food down all the time for thin cat - supervise them if feeding at same time, or feed separately. Thin cat will learn to eat more at a "sitting" and you can then properly control how much fat cat has and hopefully he becomes healthy weight cat too. You can always slip thin cat a treat or two when fat cat is not looking too.
It will always be like this, we had a pair for 14 years and there was one tubby greedy one and one slim one who waited for the other to eat first, almost like an etiquette thing. I would put 2 saucers down, fatty would wolf his whilst skinny watched on and try to eat only to be shoved out of the way etc. You cause problems if you try and change if, as one cat is the dominant one and the other is submissive. Its a pecking order thing if you like. I used to sneak the skinny one little treats like crabsticks and pieces of cheese when fatty was out. They were both lovely cats though, and I miss them terribly.
The only consolation is, they were both the exact same age, and thin cat lived 3 years longer.
Like alysonpeaches I try and sneak thiner cats extra bits when fat cats are not around. Although my fat cats do have an amazing instinct for appearing just as the food does. We have 6 cats and DH says that they all end up fat eventually. My newest 2 rescue cats are plumping up nicely!