Yeah pretty much,
The agent system isn't exactly finalised yet. As agents are types of proteins they are made in the nucleus and golgi body (I believe, seek better sources for bio knowledge ). So the plan is to have an "agent gland" which stores up agents and then fires them out in a coherent puff.
So summoning and binding should probably be either rolled in with the combat agents system (you produce and manage them with the same interface) or some kind of option you can turn on in your nucleus, or something like that. I'm not sure whether it makes sense to have them as organelles (though that would work).
It's almost unhelpful to think of a stage boundary, it's basically completely continuous. So now you go to the editor to change the organelles in a cell. When you have a colony you can go to 2 editors. The first is the one we have now, a cell editor which lets you specialise the cells. The other is a colony editor which lets you place these cells you have into different patterns.
So I start with one type of cell and just lay it out into a (probably hex) grid. Then I can go in and make specialised versions. For example you cam make a muscle cell and a bone cell etc, by editing organelles. Then I can lay out muscle and bone cells into a hex grid and my creature will soft body waggle. Does that make sense? I may have explained it badly.