Give them time. Your pup is only 9 weeks old. They may never learn to be best friends but they will learn to tolerate each other. In this case it's the cat who will tolerate the dog. You should see a major difference in about a month or so.

As for the food problem... I solved that by putting the cat food on a desk that the dogs can't reach. Cats love to jump so that really shouldn't be a problem. When you make the transition make it something the cat really can't resist. Once the food bowl is discovered in the "new" location, the cat will return when it gets hungry.