You don't need two sets of wheels unless you plan to use the bike for very hardcore MTBing in real mud. Just fit good quality backroad touring tyres like Marathon Duremes. Or Marathon Extremes will give you quite a bit of mud capability and are still fairly good road tyres. (Dual purpose tyres that work really well are new and it's a relief that they are here.)

Otherwise you need 700C rim disc brake wheels. You'll also have to specify a rim width, this will depend on the tyres you want to use. Other stuff like ideal spoke count and pattern will depend on your weight and how you intend to use the rims - will they be for road or offroad? Will you be riding fast and taking jumps and drops offroad?