There are two ways to draw reactions in JChempaint:
and draw
the reaction arrow. All molecules to the left of that arrow become reactants,
everything to the right products and everything on the arrow catalysts in a new
reaction. This illustration shows what is meant with "left", "right" and "on":

If you want to layout the reaction cleanly, just do "Tools->Clean Up" - this will layout molecules straight from left to right.
You can have multiple reactions in one drawing, for this choose "Reaction-> Make Reactant/Product in New Reaction" once you drew your first reaction. If you then do "Reaction->Make Reactant/Product in Existing Reaction", you are asked to which reaction you want to add.