How many are they running on at the moment, and out of the 3 maximum capacity, what function is each one responsible for?
They have two but one of them is severely depleted. They had none when they acquired the three that the Replicators left behind. One of those went to the Odyssey and another went to the SGC to power the Ancient Outpost. The one they kept was severely depleted after "First Strike" but they managed to steal another from the Replicators. The ZPMs are connected to the city's power grid in a room with slots for three. There's no indication that they power different systems individually.
Can Atlantis function with only one ZPM? I remember from "before i sleep" that the 3 ZPMs' had to be used sequentially rather than in parallel in order to keep the shields up for 10,000 years, IIRC. So it isn't as clear-cut as with 1 ZPM, you have shields, with 2 you have shields + cloak/weapons, etc?
^Atlantis can function just fine with one under normal circumstances. They also have a series of naquahdah generators augmenting their power supply. Atlantis can power its shield and fire drones at the same time with one ZPM, you just run the battery down faster. The city is not designed, however, to travel through hyperspace with only a single ZPM.
I made a mistake in replying to this before watching "Ghost in the Machine". They clearly say the ZPM (singular) multiple times in the episode. I guess the old one must have been completely drained.
Yeah they probably used up the one used to power the Hyperdrive at the beginning of season 4, it wouldn't have had much power left at that point, easier to use it up then switch to using the stolen Asuran one.
Rodney had to rewrite an entire section of the operating system so that Atlantis would "ignore" the fact it only had one ZPM and had to ignore all other portions of the code for the operation potentially allowing hundreds/thousands of things to go wrong, which it did, and it was only the Deus Ex Machina of stealing a new ZPM that saved them. They managed, but its not something they should have done, or should ever attempt again.