The PCM should "trim" (learn) the amount of pump duty cycle needed to get the desired rail pressure. There is a coefficient in the tune which basically gives the PCM a ballpark figure on what to expect from the fuel pump and then it "learns" from what it sees while running and adjusts on top of that...
So, particularly when you first put it in, it will be a little "surprised" by how much pressure it gets from a given command (compared to the old pump), but it is a feedback system so it should adjust. Not a terrible idea to get the tune adjusted though, so it does not have to "learn" and does not lose this info in the future when things get reset.