I think it's one recharge roll for each power, made just before the power is attempted to be used.
I could be wrong, but I've been using it like this:
FIRST ROUND
Black Dragon uses Breath (Recharge 5,6)
SECOND ROUND
Black Dragon wants to Breath again, but a roll of "4" says he hasn't caught his breath yet. So he chooses to use Cloud of Darkness (Recharge 3,4,5,6) instead.
THIRD ROUND
Black Dragon wants to try another Cloud of Darkness, but a roll of "2" means his Cloud of Darkness Power is not yet ready to go again, so instead he tries to Breath again, and a roll of "6" says he can, and he dissolves a few PCs in a spray of acid.
FOURTH ROUND
A roll of "5" says that Breath is ready again. And a roll of "3" says Cloud of Darkness is also ready again. So Black Dragon can choose to use either one.
And so on...
Sometimes both powers are available, sometimes one or the other, sometimes neither. But the DM never has to keep track of which ones are currently "recharged" or not, he simply rolls to see if a power is available.
I could be wrong, but I've been using it like this:
FIRST ROUND
Black Dragon uses Breath (Recharge 5,6)
SECOND ROUND
Black Dragon wants to Breath again, but a roll of "4" says he hasn't caught his breath yet. So he chooses to use Cloud of Darkness (Recharge 3,4,5,6) instead.
THIRD ROUND
Black Dragon wants to try another Cloud of Darkness, but a roll of "2" means his Cloud of Darkness Power is not yet ready to go again, so instead he tries to Breath again, and a roll of "6" says he can, and he dissolves a few PCs in a spray of acid.
FOURTH ROUND
A roll of "5" says that Breath is ready again. And a roll of "3" says Cloud of Darkness is also ready again. So Black Dragon can choose to use either one.
And so on...
Sometimes both powers are available, sometimes one or the other, sometimes neither. But the DM never has to keep track of which ones are currently "recharged" or not, he simply rolls to see if a power is available.