If you want to truly master the gearbox, then you need to understand how it works.
Begin by examining the power curve of your car, is the top more flat and wide or more peaky and thin?
Flat and wide: Congratulations, the gearbox is probably mostly fine as it is (this is why muscle cars can get away with only having two or three gears). What you may want to adjust is the top speed and get rid of any excessive wheel torque in 1st gear. To adjust top speed, adjust final drive or top gear (smaller number = higher speed). To adjust the amount of wheel torque in first gear, adjust final drive or first gear (smaller number = less torque, adjust this until you can barely spin the wheels in first gear).
Peaky and thin: This will take some more work to optimise. What you're aiming for is a gearbox that allows the engine to stay as close to peak power as possible for as long as possible.
Why is that? Well, we need to understand what makes the car accelerate. There are two properties of the engine: torque and power. The torque is the force that the engine is producing, more precisely the force that rotates the crankshaft, thus:
"The greater the torque, the better the acceleration."
Except that is only half the truth, because we've got a magical box that can multiply the torque for us: the gearbox. What the gearbox does is that it trades speed for torque. A ratio of 2.000 halves the speed, but doubles the torque. What this means is that torque alone doesn't tell the full story; because we can trade speed for torque, the true potential of the engine becomes the product of torque and speed, and that is what we call power.
Peak power is the point that would achieve maximum acceleration at any given speed (as long as there is traction, that is). So in terms of performance it's always beneficial to run as close to peak power as possible, even if it means that you'll never run the engine at its peak torque. In terms of fuel consumption it's better to stay at peak torque, but that's a different story...
Now take a look at the power curve again, and try to identify some key points in it. Here is an example, where torque is the Nm curve and power is the kW curve:
This entirely fictional power curve is fairly peaky, but there is a nice flat region at the top, between 5000 and 7000 rpm. When tuning the gearbox for this engine, the goal would be to try and stay between 5000 and 7000 rpm between all the shifts, and the closer to the peak at 6000 rpm the better. Before 5000 rpm there is a sharp drop in power, so avoid dropping below 5000 rpm. You can do this mathematically by calculating each ratio and what they would need to be in order to stay within the rpm range, but it also works fine to make a rough estimate and then test it to see how far the RPM drop when you shift up. As a visual guide you have the gear ratio graph, where the vertical axis is the engine speed and the horizontal axis is the wheel speed. In this case 5000 rpm would be just above 2/3rds towards the top of the graph.
If you've managed to set the gears so that the car stays near peak power but you don't get enough top speed, first see if there is any excessive wheel spin in first gear. If there is you can just reduce the final drive ratio to make the entire transmission taller. If there is no excessive wheel spin in first gear you have a difficult decision to make: at what speed does it hurt the least to reduce the performance of your car? In general, it's best to reduce the performance at the speeds where you'll spend the least amount of time during the race. At a fast track with long straights that would be 1st or 2nd gear, while on a track with only brief moments at top speed you could reduce the performance at the top gear. So what you'd be doing then is to shift the power to the speeds where you need it the most. Keep in mind that as the gears get taller, you'll spend a longer period of time in each gear, why I would advice you to try to minimize the time spent far off peak power in the top gears. Most stock gearboxes are set in this way, so the gap (in terms of RPM) between the gears get smaller and smaller the higher up you go.
Finally: Another effect of the gap between the gears is the amount of time it will take to shift gears. The bigger the gap, the longer it will take to complete the shift, as the engine will require more slowing down to match the revs of the next gear. At most this will account for a tenth or two of a second, but if you're really chasing the top times then it might be worth exploring.