OK. I understand your problem.
The three throttle wires should be on a white connector that matches one on the controller.
The main power connector on the controller has three wires: thick black, thick red connect to the battery, and the thin red has to be connected to battery "+" as well for the controller to work. You cab connect it directly to the thick red if you want, but the best way is like this:
The yellow and brown on the throttle are the switch on it, so join the thin red on the controller to one of them and join the other one to the battery "+" somewhere (maybe the thick red wire). Now the controller will switch on/off at the throttle. Next, connect the green wire to the controller side of the switch (to the thin red also) and now the LEDs on the throttle come on when the controller is on.
In simple terms, cut the thin red out of its connector; join it to the brown and green wire from the throttle; connect the yellow wire to the battery "+".
If you want, you can connect the green and yellow wires to the battery "+" instead. Then the LEDs will be on all the time the battery is on, which is useful to remind you when using lipos.