If coming from / going to the south, make the transfer at Alexandria, VA, then take any WMATA train north to DCA. If you need to go to Dulles, then you take a Blue line train north to Rosslyn and change to a Silver Line train for the long haul out to Dulles. The Amtrak station and the WMATA station are adjacent and parallel at Alexandria. (Back in the 70's when I was working on WMATA the line to Dulles was a maybe someday, but probably never extension of the system. The squawk at that time of the WMATA planning was that the DCA station was not immediately adjacent to the airport terminal as it was at that time. The terminal expansion has made it more central to WMATA.)
Just a gentle reminder that it's not yet possible to take the Silver Line all the way to Dulles. Current prediction is fall 2022/winter 2023. (See post at US Airports and Transit Connections.) Right now, you'd take the Silver Line to its terminus at Reston Town Center then transfer to a bus. Pretty good bus, from what I hear, but still a bus.