It's a fine question. The answer is yes and no.
In most everyday situations B5 operates fairly autonomously; EA doesn't
generally get involved unless there's a very good reason. And from time to
time, they do. That happens right off the bat in the pilot movie, where they
stomp down hard. They exercise other authority from time to time _
"suggesting" that a group of Centauri representatives be given the VIP
treatment in order to encourage them to invest and help to defray the cost of
running B5 (an issue that never seems to come up in TV SF...just how much DOES
the Enterprise cost to run?), and in the series, there's considerable conflict
planned for down the road between those on B5 and the EA officials (especially
since not everyone is 100% behind B5, and would love nothing more than to see
it shut down).
Wheels within wheels...that's the secret.