BungeeCord Plugin Folder vs Server Plugin Folder

I know this may seem like a potentially dumb question, but please be gentle...I am new to this.

I am using BungeeCord to make a multi-world server. At this time, it will be just a Lobby (Hub) and a survival world. BungeeCord, Lobby, and the Survival World is set up (mostly...am waiting to add custom worlds for lobby and survival world until plug-ins are working). Eventually, I will be adding more worlds (along with a hardware upgrade to go with it)...like a Factions World, Creative...

BungeeCord Plugin Folder vs Server Plugin Folder