what would that entail if the character could control compounds as well as elements?
whole compounds give more freedom of movement. for example, let's take methanoic acid. its formula is CH2O2. if your character could control elements only, she would have to control carbon, hydrogen and oxygen separately. I imagine that would be more time-consuming or energy-intensive. if she could control the whole compound, it would be faster for her to move it somewhere else, but, I think, harder to do reactions. but that's just my assuming! maybe defining pros and cons of this dilemma won't change a thing about how she does her reactions, but I think it's the basic thing to know that will give you a starting point.
what would happen if you messed with the elements inside a plant well it grew? could you make it grow faster or change the plant completely?
you could definitely kill a plant in many ways, just by taking H2O, H+, ADP, NADP+, even electrons, and the list goes on. I don't think you could change the plant into a different one, and if your character could control such big compounds as one of those huge chlorophylls like here:
it would only change the color of the plant, and she'd have to move lots of those. UNLESS she could somehow control the billions of billions molecules of DNA, and change all of them at will. but that's a lot of work and knowledge about proteins.
making a plant grow faster would be possible, but that would be a long and monotonous process. you'd have to constantly give light, carbon dioxide and water to a plant, improve the productivity of all thylakoids in all chloroplasts in all cells, speed up the transport of organic compounds and many other reactions. that's a very complicated process from a biological point of view, but if your character could master controlling all those reactions, they would be possible until the resources run out.
what kind of reactions cool down things? like what could you do to freeze water?
this one is the easiest question - everything that needs to be done is to slow down the movement of atoms. every atom in the world moves at an enormously high speed. atoms in the gases move the fastest, slower in liquids, and in solids they only vibrate. I found this picture to help illustrate it better:
the faster atoms move, the higher the temperature of the body is. so if your character could slow down their movement, she could easily control the state of matter of every element (and I think even regardless of the air pressure and temperature)! remember, even if she turned water to ice when there's 25°C outside, she'd have to maintain the process, because the ice would obviously melt.