How to target a train summoned via TrainCarts plugin and then /entitydata to set its passenger(Armor Stand)

The best place to find support outside of vanilla would be wherever you got the plugin (presumably here).

However, if you're playing in 1.9 or later you can use the following command to add a passenger to your minecart: /entitydata @e[type=MinecartRideable] {Passengers:[{id:"ArmorStand"}]}

Note that the above is a Mojang-provided command and may or may not break your Bukkit plugin.