When in manual mode, the camera actually still meters using the set metering mode (multi-segment, center-weighed, average, spot, etc). This is shown in the exposure-meter which usually displays EC. In manual mode though, the camera shows the difference between the metered exposure and the set exposure.

Now, if you change your exposure until the indicated difference is 0, you've missed the point of using manual exposure. Well, in some cases, such as for stitching panoramas, this is actually useful, but generally manual mode is to decide your own exposure.

The way you set it depends on the image you want to create. Aperture controls depth-of-field, shutter-speed controls the rendering of motion, so set them as you need to realize the image you want.

Once you set the parameters needed (A or T or both), you need to figure out how to set the remaining parameters to create an image of acceptable brightness. On some Pentax camera there is a semi-automatic called TAv which automatically sets ISO according to a set aperture and shutter-speed.

To set the remaining parameters, look at your subject and decide where to meter. The most pleasing way of doing this is to meter on the brightest part of your subject and add +3 (or so, depending on the dynamic-range of your camera) to make that part bright and everything else should fall in place. On Olympus DSLRs there is a metering mode called Spot Highlight to do this automatically. If the results are too dark, then you've exceeded the DR of your camera and are going to have to blow some unimportant highlights (if there are any).

For the action of metering you may be able to do it in manual mode using the AE-L button or the Green button (on Pentax). Otherwise you can use an automatic mode (P, A, S) and then dial in the same values in manual mode as a starting point.