I plan on running both salt and freshwater next year due to the drought we are having here. Should I get a set of Aluminum anodes for the salt and a set of Magnesium for the fresh water and change them accordingly or could I get away with just one set? If I could use just one set what would be the best, the Aluminum or Magnesium?

If you are not leaving the boat sit in the water more than a day, then you don't need to worry about it.

Where do you plan for the boat to be moored? Use THAT for your anode choice. If it's a mixed bag, then go with zinc, as it is the only choice that is sacrificial in both environments.