I'm going to go with each one individually, but can control all of them as a whole,.
Annabeth scanned the sky. "That's why I made a plan with Frank and Hazel. Hopefully... ah. Look."
A bee zipped overhead. Dozens more followed. They swarmed around a column, then hovered over the opening of the pit.
"Say hi to Frank, everybody," Annabeth said.
Piper waved. The cloud of bees zipped away.
"How does even work?" Percy said. "Like... one bee is a finger? Two bees are his eyes?"
"I don't know," Annabeth admitted. "But he's our go-between. As soon as he gives Hazel the word, she will -"
"Gah!" Percy yelped.
The Heroes of Olympus, book 5: The Blood of Olympus, chapter 42
But that's not the first time we see Frank turn into a swarm of bees. He does it in The Mark of Athena too:
Piper had a gag in her mouth, so apparently the dolphins had discovered she could charmspeak. Frank was the only one missing, though two of the dolphins had bee stings covering their faces.
Could Frank actually turn into a swarm of bees? Percy hoped so. If he was free aboard the ship somewhere, that could be an advantage, assuming Percy could figure out how to communicate with him.
The Heroes of Olympus, book 3: The Mark of Athena, chapter 30
The key point here is the bee stings - Frank has to be able to control when each bee individually stings, otherwise his entire swarm would sting at once and he'd die. He has to sting when the right bees are in the right place, which requires being able to control each bee individually.
And as we see in the first quote, we see a single bee zipping, and then the rest of the swarm. He has to be able to direct each one to know roughly when to turn each bee, so that the swarm can move - if it had to move as one big unit, that would greatly hamper Frank's ability to move around as a swarm of bees.
Aside from that, we don't know much about his bee transformation ability, as the quote from The Blood of Olympus shows.