A method of controlling a plurality of marine drives on a marine vessel includes detecting that at least one of the plurality of marine drives and that at least one of the plurality of marine drives is not running, and then determining, based on the trim position of each of the at least one non-running marine drives, that at least one non-running marine drive is trimmed down. If so, an output limit restriction is effectuated for each of the at least one running marine drive and an alert is generated to advise an operator of the output limit restriction.