Looking at the flowrate charts for each pump, I don't see much of an upgrade. At 0 ft , the mag 3 pushes 375 GPH while the MJ1200 pushes 295 GPH. The mag 3 also uses 75% more wattage to gain just 27% (80gph) more water flow.
However, if you still wanted to make the move, simply get the correct size tubing to make the connections. The mag 3 discharge outlet is 1/2' MNPT.
With the CPR Bak Pak skimmers, you need a RTV type pump which allows you to draw air from the intake side of the pump. Rio does this with their 600 & 800 pumps and Maxi Jet adds a doo hickey with an airline attached. The AquaC Remoras are different, they use a spray injector.
CPR Bak Paks come with an RTV Rio 600. The recommended upgrade (by CPR) is the Maxi-Jet 1200 with venturi attachment. For some reason they did not recommend the RTV Rio 800.