Just copy and paste the CLEO folder to your GTA Vice City root folder. This mod requires the CLEO Library to run.
Press 1 to enter the Vehicle Spawner menu. Press 'Left/Right' to scroll through the vehicles list. Press the 'Action' button to spawn the vehicle you currently have selected.
You can change the primary color of the vehicle with the 'Up/Down' directional buttons, and the secondary color with the 'Next Weapon/Previous Weapon' buttons (only works after the vehicle is spawned). The vehicle will be spawned with its regular colors until you press one of these buttons, so you can just leave the default colors if you like.
To exit the menu, just press the 'Enter/Exit Vehicle' button. Alternatively, you can press the 'Weapon Fire' button to be put inside the spawned vehicle right away. If it's a helicopter, you'll be instantly put high in the air, while with a boat or the Skimmer you'll be put on the water next to the jetty on the Starfish Island mansion.
The vehicle will be spawned right in front of Tommy, so make sure the space in front of him is empty (don't stand close to a wall or a building). If there's any ped or vehicle there, they will be erased (which will most likely crash the game if a key ped/vehicle during a mission is erased).
Press and hold 2 to make the mission name appear on the screen. Press the 'Next Weapon/Previous Weapon' buttons to scroll through the mission list. While still holding 2, press the 'Action' button to start the mission.
DON'T SAVE your game after playing through a mission this way, even if you have a 100% completed save. Some missions that take place on a building that's closed/destroyed may be unplayable (or even crash the game) depending on your game progress.