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I suppose that answers most things, but why is it that even when I have more water and energy, the arrow from that side, and hence profit, doesn't go higher? It stays below.

ok I see. The white graduations (bottom left) indicates sap units, you must have energy and water bars above one graduation to produce a new unit of sap.

More precisely, you need several units of water (say 3) and energy (say 5) to produce one unit of sap. So if you collect 12 water and 9 energy you still produce only one sap and blue bar is 9 units above white line and yellow bar 4 units above.

You really should state that somewhere. It took a month for me to find that out, before it looked very random.

Indeed it's not really clear. I added one line about this in the Respiration section, maybe it's not enough and could be better explained but I don't want to overload the documentation (i'll do a complete guide later). Thanks for pointing this out.

It'd probably be considerably better if there was an indicator for the amounts of sun/water needed to up the production, or if there were floating point numbers here, rather than only integral amounts of sap being produced.

I chose to use natural numbers to represent the photosynthesis (it seemed to me more logical) but indeed it's disturbing and finally with floating point numbers it will be much clearer. I'll try it (currently I am a little overloaded :/ ). Thanks!

Yeah, it turned out pretty confusing :P

No worries, good luck with whatever it is that's overloading you!