Using an IC card and tickets when several transport operators are involved

I'm piecing together a Japan trip with city trains, a regional railway and a longer-distance train. I know an IC card can pay for many ordinary rides, but it isn't a magic ticket for every service. My worry is reaching a gate with the wrong thing loaded after changing operators. If a trip involves a limited-express surcharge or a reserved seat, what should I check before boarding? I'd rather learn the distinction between base fare and extra tickets now than on a crowded platform.