The muscovies are better foragers and crave more meat than other duck breeds. So, they are better for controlling slugs & crawly things. They are also sometimes called "quackless" because they aren't noisey like all other ducks. The meat from the Muscovy is considered the best by many people...
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I wouldn't mix the two until the muscovies are at least half the weight of the pekins. Otherwise they'll never get any food. I haven't ever found my ducks to be agressive to other waterfowl (whereas mixing Geese can be really tough).
Make sure you let your pekins see the muscovies...