ORIGINAL: HerpInYourDerp
You just need 1 cell. It'll automatically reload itself from the planetary stores if it runs out.
Not all bases are over colonies. I was wondering what happened to these so I've tested it.
I carried out two tests using a simple monitoring station, one with and one without a cargo bay and with no energy corrector. The pic shows the base design with a cargo bay and it's position in a system. The blob to the SW (if there is a SW in space) is a freighter loaded with 600 Caslon, the max load of the freighter. As you can see the base has no fuel yet and there is nothing in the cargo hold. Once the freighter docks fuel tanks are filled up and the remaining fuel is placed in the cargo hold, This was actually the second test.
The first test followed the same set up except the base had no cargo bay. This time the freighter was carrying only 65 Caslon, the fuel cell capacity. The freighter docked and emptied it's tanks but I have no idea where the fuel went. The fuel cell remained empty and with no cargo bay I can only assume it was 'dumped into space'.
Conclusion
Fuel cells are filled up from the cargo bay.
Not tested, but suspected.
As others have pointed out, when over a colony a base will draw from the colony but not direct to fuel cell, it goes through cargo bay. I'll test this next.
Unexpected result
You need a cargo bay to retrofit. I read this before and have always put a cargo bay on all bases but the first monitor station didn't and when it came to retrofit to the Mk 2 with a cargo bay I waited and waited and waited... I scrapped it and built a new one. If waited some more maybe it would have?
An oddity
The Long Range Scanner appeared to work all the time even without any fuel. The scanner required 60 static and without an energy collector I expected it to draw on the reactor to work. But with no fuel the reactor can't (or shouldn't) work. Don't know why or if I made an error but I'll try this again.
