I've been playing the GT series for 12 years now, and up until GT5P I had been a manual transmission purist. But now I almost race exclusively with the auto transmission, especially in Ferraris. I employ the technique my driving instructor at Skip Barber imparted on me, "Either you're full on the gas, or you're full on the brake." Now there are certainly times when you trail brake, or feather the throttle, but using the automatic transmission, you really need to pay attention to braking and your apex. I've also found, even when using the manual transmission, some lower speed corners are faster using the gear one up from the recommended gear, especially through the S's in Suzuka. I've driven Suzuka with manual and automatic, and I can never catch my ghost car when using a manual transmission.
Despite my recent preference to use the automatic transmission, the manual is a lot of fun when racing online, in a close race. I especially love driving the Integra with a manual transmission; I love having complete control of that beautiful sound of a high-reving honda.
Some people talk about engine breaking, but that would put excess wear on your motor in the real world, especially if you're hitting the rev limiter. I drove Formula Fords in Skip Barber at Sears Point, and they had a 4-speed transmission with no sycro-mesh, so you had to double clutch. The concept was extremely intimidating, the thought of having to use the clutch twice as often as you're used to, while braking into a hairpin at over 100 miles per hour, seamed impossible. But before you knew it, it came as second nature, as you become in-tune with your car.
Sorry, old people tend to rattle on.
Don't let the manual transmission intimidate you, you'll appreciate the added control you get, and be all the more satisfied when you win races knowing that not only did you drive a faster line, and had the right braking points, but you hit your shifts right also.