By default, the D90 uses the Matrix Metering mode. It's very smart, even if your scene has very dark areas combined with well lit areas. It covers the entire viewing area, sees in color, and has pretty good depth perception. I think you'd find that most photographers use this mode 99% of the time. The other metering options (Center Weighted and Spot) are more or less holdovers for old school shooters. You first might want to make sure you haven't accidentally changed your metering mode.
Nikon suggests that you don't use the Exposure Compensation button w/ Matrix Metering, but I (and I'm sure others) do it all the time. The most important thing to remember is to make sure you're starting at 0.0...and be sure to change it back to default for next time if you do end up changing it. I use the KISS method when it comes to setting exposure. You'll find hundreds of technical tips on the internet and in books on how to do it correctly, but I just take the shot and look at my LCD screen and make adjustments accordingly.
I also have access to ACR (Adobe Camera Raw) and Photoshop...and can tweak exposure there if need be. Though it's always best to do it at the camera. For the most part, the only consistent situation where I've used Exposure Compensation is indoors where lighting can be tricky. These days, I almost always use a remote or on-camera flash, even in the daytime, when indoors because I can control my lighting better that way.