When you upshift check wher the rpm goes to when it chages gear and starts accelereating again. When decelerating shift down when it gets to that Rpm. Also just keep practicing the more you drive in manual the more you'll be able just to sift by ear rather than watching Rpms.
Up/Downshifting is different for every car. Basically you have to look at the power curve for the car in the settings. If you go below X rpm that is below the peak power then you want to downshift so that your rpms are back as close to the peak as possible. Same applies for upshifting, don't wait until you hit redline to upshift if you're going to end up past the peak power that the car can make.
Having said all that I use manual in the game, I just feel like I have more control over the car. I've also found that I can go faster around a track with a manual over the auto.
In real life I also drive a manual, it's in a '98 3000GT. GT4 has got it kind of messed up though, at least for 3000GT's, they have the styling on some of the years mixed up.
