First of all you need to know what each setting means. It helps when you are in manual mode and things are too bright etc. Try reading up in your manual to get a little idea.
The F number (aka aperture) goes like this. If your F number is really high, like F11, less light will get in. If you have a low F number, such as 4.0 more light will get into your camera, sometimes making your photos too bright. ISO kind of has the same effect. Lower your ISO and less light will get in. I'd suggest not maxing this one, as it does create lots of "noise" in your pictures (it does on my camera anyway). I mostly use ISO 100-800 depending on the situation.
And don't forget about your shutter speed! The slower your shutter speed, more light does get in, but sometimes you need to use a tripod for that. Especially doing night pictures or taking photos in dark places. Read up a little on shutter speed, it still confuses me.
What I do in Manual mode is normally set my ISO and F number to what I want, and use my shutter speed to make it so it won't be too bright/too dark. There's a meter in your view finder that you can go by; that should also be in your manual.
That's the best way I can explain it. There's more technical ways to explain it but those are hard to understand for beginners

I know I had troubles.