To set this up, I have two guerrillas in a space with an event that allows for me to take cash from another opposing piece. One of my two guerrillas are active due to a terror operation during the same turn. Do I have the choice of which of my guerrillas receives the cash?
Also, does it matter, since if the active guerrilla is removed in a subsequent turn then I would merely move cash from the active guerrilla over to the non-active one. Right?
What event card are you talking about?
I have to assume some things you left out of the scenario. I assume you mean that there is an opposing piece that has a cash marker in that same space? If so, then yes you can put the cash marker under any of your guerrillas.
You are also correct that if you put the cash marker under your exposed guerrilla X, and later it is removed, you can move the cash marker to a different guerrilla Y at the moment that X is removed. (In fact, you can move the cash marker to any piece in the space not just your own.)