Ultimately the same. They do a good job of getting ammonia to nitrate, but eventually you need to get rid of the nitrate. Skimmers are real popular because they haul out tons of organics before they ever start to turn to ammonia, and so reduce the filter load. Shops will sometimes tell you they're not necassary for FO tanks, but they're a good, good addition.
I think for the 29 salt the whisper 40 will be absolutely hopeless. How many gallons an hour does it shift. In total a number of 10 x tank volume or 300 gallons per hour wouldn't seem unreasonable, or look it. You could always take the magnum 350, use it for biofiltration, and a place to keep carbon, and by arranging the return through a spray bar use it provide water movement.
Once you get your water movement up to scratch you get into a position where your sandbed and liverock are doing your filtration for you, not your 'biofilters'