when you scrape your original sample onto your agar plate, you cannot see how much single bacteria or where the individual bacteria is on your plate- since it's invisible to the naked eye. But when the bacteria start to multiply, you start to see the individual colonies. (from the single bacteria, it begins to multiply within 20 min. maybe after 1-2 days you'll see a colony, meaning there are millions of bacteria)
for example, if you take a water sample and spray it onto an agar plate, you won't know which parts of the agar plate the bacteria landed on. however, when they start to multiply from a single bacterium, you'll see where each starting bacterium was because now you can see a whole bunch of bacteria. (remember that a colony contains millions of bacteria- which allow it to be visible to the naked eye).
so you count the number of colonies, and that'll tell you how much bacteria you started with. if you look at the size of the colonies, you're only looking at how long you allowed the bacteria to incubate (since from the single bacteria that you started with, it's only multiplying and growing outwards).
