They probaby use smoke signals or railroad whistles
Yes the Switchboard was the main base for the Railroad at one point, and at some point you will get to go there for a RR quest. The switchboard fell during a large scale attack on the RR by the institute, with any other bases that the institute knew of being attacked around the same time.
With regards to the dead drops, I suspect they have some kind of signaling system that notifies them that a message has been left in a dead drop and which dead drop has been used. It may be radio, or a light being switched on, or an object being placed in a certain position.
You should have already been there. The Switchboard is the place you go to with Deacon during the Tradecraft quest, right by the Corvega Assembly Plant and Super Duper Mart in Lexington.
I assume they have some kind of radio contact. I believe there's always someone sitting at a desk operating a ham radio there actually. Though I may be remembering that wrong.