What you control:
1. Shutter speed
The slower the shutter speed, the higher the fstop you'll need to use for a proper exposure
The faster the shutter speed, the lower the fstop you'll need to use for a proper exposure
Manual Mode is where it all comes together: you're now choosing everything, the camera is deciding nothing. Remember: shutter speed and aperture are bound together: when one goes up the other must go down, and visa versa. I personally rarely use manual mode, except for when I'm shooting night photos - but you may find that there's a reason that you'd like to use manual mode.
One thing to note about aperture, which is illustrated in the aperture chart in the Aperture Priority section: the lower the number, the more that will come into the camera when the shutter is open, due to the larger opening for light to come into. If you need more light but can't use a longer shutter speed, increase the size of your aperture: by lowering the f-stop. Use your LCD to see how your exposures are looking, and adjust accordingly, based on what you learned in both the Aperture Priority and Shutter Priority sections.
If your images are too dark, you need to let more light in by either using a longer shutter speed or a lower f-stop (or by using a higher ISO). If your images are too light, you need to use either a shorter shutter speed or a higher f-stop (or by using a lower ISO). Don't be too obsessed with getting perfect exposures on Manual: let the camera do the work for you in Program (P), Shutter Priority (Tv, S), and Aperture Priority (Av, A) modes especially early on. And remember - have fun with it: the more you work on all of this the quicker and more naturally the adjustments will come, and the more you'll feel comfortable doing - enjoy!