Very carefully! You really want to use the wiring diagram that should be on the inside cover -- can you send us a picture of it?
Check, double check, and triple check which side is high vs low voltage. The high voltage wires may actually be thinner than the low voltage wires, making you think they should be the opposite, even if you're an electrical engineer like I am (albeit on very low voltage circuits!) and should know better -- a given wattage at higher voltage results in less current, thus smaller wire requirement, than the same wattage at lower voltage. Reversing them will instead of sending 12V to the lights send 1200V, and will probably blow the bulb or LED assembly and have you puzzling for hours before you reread the diagram and smack your head. Don't ask me how I know that!
Most of the Intermatic transformers (I have a PX100) seem to have the high voltage on the left, with the multiple wires to select different output voltages on the input side (which contributed to my confusion). Some brands have it the other way, and the fact that the instructions say to find the wiring diagram on the cover make me think that not all versions of even the Intermatic are the same.
In any case, you'll connect the 120V line voltage to the high voltage side in the high voltage comparment using the white wire and just one of the black/yellow/blue wires, depending on the desired output voltage. The pool light connects to the wires in the low voltage compartment.
Another note -- all of those wire nuts and connections should be in the lower left or right compartments, not in the upper transformer compartment. The purpose of these listed transformers is that they're designed to isolate possible faults (e.g. wire nuts coming loose) so they can't accidentally send 120V through to the light and the pool.