It depends on how the generator is wired.
My generator head is a 2 coil unit, as are most 120/240 generators.
The coil leads are all connected to a switch. That switch's position determines if the coil's leads are connected in a series or parallel arrangement.
Here is a photo I found online that demonstrates it.
As you can see, with the switch flipped to 240vac mode, you get the graph on the left where the lead #'s 2+3 are connected to form a common neutral, with 1+4 having 240 VAC difference.
With the switch flipped to 120vac mode, you get the graph on the right where coil lead #'s 2+4 are connected and 1+2 are connected, giving you 120vac difference across the wire pairs.
Now, back to your question. You can wire it in a way to get one single 50 amp source, because the 2 coils are already connected together. But I don't think you'll be able to power 3 ac units off a 5500 watt generator. Typically, you'd run something that large off a 10kw unit because each ac unit requires around 3000 watts at startup. The minimum size they spec is 2800 startup watts per unit, and you'd still be well over 5500 watts with 3 units. So the most I'd run off yours is 2. And you can do that with the 2 circuit system you have.