OK, here are the basics of manual flash photography, assuming we're going to be using the flash as the main light source.
First off, the shutter speed has no effect on the flash other than that it should be set to max sync speed or lower. There are some flashes that have high speed sync that will allow you to use the flash at shutter speeds higher than max sync speed but I'm going to keep this post simple and just ignore them for now. For most purposes, a shutter speed of 1/60 to 1/200 or 1/250 is appropriate.
The next consideration is the aperture you want to use. This has a direct effect on the amount of flash light that is registered by the camera and hence affects the working distance of the flash for a given flash output. Aperture is usually determined by the DOF you want in the photo.
The third consideration is the ISO used. The higher the ISO, the farther the working distance of the flash becomes for a given flash output. ISO and aperture go hand in hand when using the flash in manual mode as they both affect the working flash-to-subject distance.
And the forth consideration for using the flash in manual mode, for those models that have this feature, is the flash power output setting you want to use. The flash output also determines the working distance of the flash.
The aperture and ISO settings you use can be determined after giving some thought to the resulting photo you would like to get or, as some people then to do, just set arbitrarily because that's the setting they always use when the camera is set to manual mode. 
But it is the flash-to-subject distance that will ultimately determine how the camera and flash are set up. This is because, for a given power output of the flash, there is only narrow range of flash-to-subject distance that will properly expose the subject. Move the subject a couple of feet away and he'll be underexosed. Move him up closer by a couple of feet and he'll be overexposed. What this means is that if you are going to be using the flash in manual mode, you need to be good at estimating distance or have a distance measuring device that can give you the flash-to-subject distance. If not, you'll probably end up taking several shots and checking the histogram after each one to check the exposure.
So, how do we use the flash in manual mode, you ask? To keep this simple let's assume that we want to use an aperture of f/8 because that'll give us an acceptably deep DOF. Let's also assume that we've selected a shutter speed of 1/60 since we'd like to get as much ambient lighting in the picture (we're indoors at night) and still be able to handhold the camera with the lens we're using, say a 50mm lens. ISO is set to 100. So, we have the camera in manual mode at f/8 @ 1/60 and ISO 100 using a 50mm lens.
Now, say you want to take a picture of your subject that is 3 meters away from the flash (Speedlite 580EX). The guide number of the 580EX is 42 (meters) at ISO 100 and 50mm.
The aperture (f) required for a subject so many meters (d) away for a given guide number (GN) is:
f = GN / d
or
f = 42 / 3 = 14
We therefore need to set the apeture to f/14 in order to get a properly exposed photo.
If you can be flexible with your aperture choice, then you can change the aperture setting of your camera from f/8 to f/14.
However, if you insist that it be set to f/8, then you have to adjust some other setting to get the correct exposure. You can:
1) move the subject so that he's a little farther away.
You would have to place him or her about 5 meters away (42/8 ) instead of 3.
2) decrease the output power of the flash.
If you decrease the power to 1/2, the GN changes to 29.7. This will give you an aperture of 9.9, slightly overexposing the subject if f/8 is used. Or, you can decrease the power to 1/4, giving you a GN of 21 and an aperture of f/7, slightly underexposing the the subject at f/8.
3) ISO can't be changed in this case since we're already at ISO 100, unless you wanted to try ISO 50 if your camera supports it. However, if the subject were farther away and beyond the reach of the flash at full power, then ISO can be increased to give you more reach.
4) do a combination two or more of the above.
If all the calculations shown above seem overbearing, fear not! The 580EX and the 550EX, in conjunction with the camera, can do all the calculations for you. All you need to know is your flash-to-subject distance and the camera and flash will do the rest for you.
When the flash is set to manual mode and the flash head is pointed straight ahead (i.e. not in the bounce position), you will see a single segment bar above the distance scale on the flash LCD. This bar indicates the distance the flash is good for for the camera settings (aperture and ISO) and the flash output power selected. If you change any of these settings (aperture, ISO and power), you will see the bar moving along the distance scale. The idea here is to make adjustment to the settings until the bar is over the distance mark that matches the flash-to-subject distance. If you have accurately determined the flash-to-subject distance, you exposure should be spot-on.
If you want to use the flash in bounce mode, you can still use the camera and flash to help you with the settngs. Before moving the head for bounce, leave the head in the straight-ahead position and determine the required camera and/or flash settings as described in the previous paragraph by using the flash-to-ceiling/wall-to-subject distance and then add about a stop more exposure to account for the bounce and loss of light.
