In general, you can look at the Supreme court checking congress (by overturning unconstitutional laws), congress checks the president (through investigation committees, and eventually potential impeachment) and the president checks the Supreme court (by appointing justices). There are some smaller checks that run counter to this order (like the President can veto congressional bills), but they're much more minor powers. Most of the time, the "checking" of presidential power by the supreme court happens by the court striking down laws passed through congress that the president has thrown a considerable amount of political weight behind (think many of FDR's new deal programs, some of which were struck down by the court. Obamacare also narrowly had some of it's components struck down by the court). The Supreme court can strike down executive orders that are unconstitutional. President Trump's muslim ban, for instance, had some of it's elements stricken down by the court in just the last month. <span />
