The numbers underneath the organelle options indicate how many of that organism you need to engulf, but it’s not particularly clear - a high number could be good instead of bad, to someone who didn’t know how the system worked. That should be more clear.
You should also have some sort of indication in-run that a specific organism over there is actually the one you want. It’s hard to tell.
I agree, when I was first using endosymbiosis it felt confusing. I could see the fossilization icon feature being reused to mark your endosymbionts to capture.
When implementing the GUI I was thinking of having some kind of time indication on the costs, but it would have been pretty difficult to fit into the code design and I didn’t have an icon so I didn’t do it at the time. I’ve opened an issue for this now: