After clearing customs, we plan to take taxi to Atocha station for our AVE train to Valencia. Any advice about how to navigate locating the taxi location at airport and where it’s best to be dropped off at Atocha? We already have our train tix.
You don't say which terminal you're arriving at. But assuming it's T4, there is a taxi rank on the ground floor, the same floor you exit customs from. It's just outside the building and - I'm sure - is signposted.
For Atocha it doesn't really matter where the driver drops you, unless you're in a terrific rush, but the AVE trains to Valencia depart from the ground level, so you could add "planta baja" to ask him to use the rank on that level - although that's likely where s/he'd go anyway.
Follow the signs for ground transportation after coming out of customs. The signs are easy to spot for taxis, metro, and rental cars.