Click the pizza (in the top-right) the get money! The upgrades on the right are clicker upgrades. The upgrades on the left are automatic upgrades and toppings.
NOTE: Other than getting the things to the front layer and making it look good, clicking on upgrades twice is useless (same thing with all my other clicker games, they just don't overlap). NOTE: You have to click on the crust to get the money.