Just one person has to pay base rent. However you can switch the premissions so that any level can pay the base rent. And to pay it you have to go to Atlas Park, Freedom Plaza and see the man out the counter and pay it via him.
Hope that helped 
OR if you're a Villain go to Port Oakes and see the SuperGroup Registra. You should be able to pay him.
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I feel I need to ad this although you may already know.
DON'T pay upkeep right away every time it asks you to!!!!
I would set the permission to a level where not too many people can pay it.
The reason for this is that it will ask you to pay the upkeep two weeks after you paid, your base will however run fine for 6 weeks (I think, It's been a wile since I last counted) the permission thing is there to not have your lower ranked members pay the upkeep every time it asks them too, they will go pay the base upkeep thinking they are doing good and keeping the base active for the SG/VG, when in fact they are flushing the hard earned prestige down to hydra territory.
Slatecinder lvl 50 Fire/stone tank
Astrum Rangers/Seekers of Pandemonium
One hell of a favour. Arc ID: not published at this time
So, i stopped playing some time ago. And now i want to start again, but my base's upkeep is of course due, fast questions.
Does all the SG chars pay for this or only the leader?
And does the it get paid automatically or fo i need to go somewhere to pay it?
thx in advance