Exactly. In your case, any three-wire (with neutral) high-voltage appliance needs two CTs. If you have 208V appliances without neutral, there is a way to handle them with one CT.
But there’s more. All of your 120V circuits that are on Main_B have to be specified as Phase C. They will read about half otherwise (cos 120°). So you might want to first identify which of the mains is Main_A and which is Main_B.
Your load center appears to have 13 horizontal rows of circuit breakers. Most of them have double breakers on them. The phase of the circuits on each row alternate as you go down. Whatever Main is the lower of your mains circuit breakers corresponds to the same phase as the top breaker on the right side. For the sake of this discussion lets say it’s Main_B and so it’s phase C.
The next row has an empty slot on the left and the right breaker will be the same phase as the upper main, so that will be Phase A.
The next row has a GFCI breaker on the left and half of a 40A pair on the right. Those are Phase C.
Now the next row is Phase A, but it has double breakers on both sides, so all four of those circuits are Phase A.
And so on. So this is a little bit of the split-phase logistics to the panel layout, but three-phase when it comes to voltage/phase reference. This is timely because the latest release just out has improvements that apply to exactly this kind of service. IoTaWatt can deal with everything in there.
I have you using derived voltage/phase reference. You can add another VT to get a direct voltage and phase reference for the other leg. You would need a convenient receptacle that is connected to Main_B. My recommendation would be to get it all going correctly with derived and see if that works for you.
You can combine any number of conductors on the same phase to economize on inputs. Your order went out today. I’m guessing the 100A CTs are for those 40 Amp breakers. Since you will only be able to measure one side, you could use 50A for those. Judging by the black/white conductors on the upper right breakers, I think that’s a two wire 208V circuit, probably an AC compressor? That can go with a single 50A CT. Those with red/black are typically three-wire and require two 50A CTs.
If you want to return the 100s for more 50s, I can do that. If a 100 will fit comfortably around your mains, you could swap the two 200A for five 50A.