Yes, you can do that. But the direction the wires go through is important. If the currents flow in the same direction, they add, if they flow in opposite directions, they subtract.
What are you using to measure the current? If you have an emonTx and emonBase, or an emonPi, or emonCMS, you can add and subtract power in software.
Make certain that the current transformer is not a tight fit on the wires. If you force the current transformer closed, you might break the brittle ferrite core, and then the transformer will be useless.