One way to think of moles is as a counting unit. For example, when you go and buy doughnuts, you generally say "I'd like a dozen doughnuts," not "I'd like 12 doughnuts." With moles, you'd say "I need a mole of carbon," not "I need 6.022x1023 atoms of carbon." Molarity is simply moles in a liter of solution. So if you have a one molar solution of hydrochloric acid, it means that in one liter of the acid, you have one mole, or 6.022x1023 molecules, of HCl. When looking at chemical equations, they are generally written in terms of molar quantities. (Though when you're first learning them they try and teach you to have whole numbers in front of each molecule/atom, thus representing the reaction on a molecular scale). But in the following equation, the whole numbers equal moles of the following molecule.
2H2(g) + O2(g) -> 2H2O(g)
So we have two moles, or 2(6.022x1023) molecules, of hydrogen gas reacting with one mole, or 6.022x1023 molecules, of oxygen gas to create 2 moles, or 2(6.022x1023) molecules, of gaseous water. Does that make a little more sense now?