These buttons set JChemPaint into a mode to set atoms to elements. They all operate the same: Some element is chosen, all selected atoms are changed to this and you can change atoms then by clicking on them individually. There are different ways to select the element:
Here you can select the element directly
This opens a periodic table of elements. Hovering over the fields shows additional informations. Clicking on one sets JChemPaint to this element, as if you would have selected it via a button directly.
This button enables you to enter an element symbol (e. g. "N" or "Cl", capitalisation is not considered) as text. After that, you are again in element mode as if you would have pressed a button directly. If you click on atoms in this mode, the input box appears again. You can then also select from a choice of functional groups to replace the atoms with.
These buttons increase or decrease charges of atoms by one. The button changes the selection. It also switches to a mode where clicking on atoms changes charge.