ISO works similar to how film was ASA rated. In a digital camera, every doubling of the ISO setting is equal to a doubling of how sensitive the camera's image sensor is to light.
The simple answer to your question is if you can't see a difference, don't worry about it. Ignorance may be bliss here.
The more detailed answer:
Noise in the digital world is like grain in the film world. The higher the ISO or ASA speed, the more noise or grain, respectively, would be found in the final product.
I've looked through a portion of my collection and I haven't found a suitable sample to show you, as I tend to prefer very clean images, and my camera choice also tends to produce little or no noise. Noise can also be created or reduced by what is done in post processing of the digital image.
If you look at your images at 100% size, which is much larger than what you see when the image is entirely displayed on your computer screen, you might notice a texture, or graininess to the image...particularly when you look into areas of fairly uniform color such as skies. This is noise. It has to be pretty bad to be seen at the size of photo that generally gets posted on this message board, and if you make a print smaller than 8x10 you'll probably not notice it either unless you know what to look for. Perhaps ignorance is bliss?
Noise, and image quality, are things that get lost in the marketing hype promoting the number of megapixels a camera has. If 8 MP is good, 10 MP must be better right? Not necessarily...particularly when those extra pixels of resolution are crammed onto the same size image sensor. Noise increases with pixel density...particularly on entry level dSLR's. This doesn't mean the 10MP model is inferior to the 8MP model overall. It means megapixels are not the end all statistic we are lead to believe it is.
Your understanding of aperture is pretty good. Realize that higher f-stop numbers will bring more of the image into focus (or as photographers would say increase the "depth of field"), but will also result in a loss of maximum sharpness in the sharpest part of the image.
There are a few misconceptions in your last sentence. If you'll allow, I'll try to address those.
You asked "If i want to shoot low light distant objects I want a higher fstop and slower shutter speed. and I always want the lowest ISO(200 for the D40) I can go with?"
You are more than just an aspiring photographer, you are also an aspiring artist. In the world of art, there are no absolutes, and rules are made to be broken in the name of artistic expression. In time, perhaps, you'll move beyond viewing yourself as a camera operator, and view yourself as a creator of moods...using your photographs to convey more than just "on this date and place this thing was there". To say "always" when it comes to art is much too limiting.
Shooting "low light distant objects" is fundamentally no different than shooting any other subject, though it presents different challenges. One initial goal with any photograph is to get the exposure correct. You're working with Manual mode now (congratulations for exceeding the ambition of 90% of dSLR owners b.t.w.
) and you've realized there are several ways you can get a "correct" exposure though different combinations of shutter speed, aperture, ISO, and addition or subtraction of light. One of the next steps in your skills development is learning which method of exposure best suits the subject and mood you are working to create with your photograph.
I have a love of night photography. I enjoy making urban scenes at night. Sometimes I like to convey a sense of motion in my photographs. Oftentimes people walk through the scene as I'm taking the photo.
For all the reasons above, I tend to shoot at small apertures at night. Architectural images seem to work best in my opinion when the majority of the image appears to be in focus. Noise can be reduced with lower ISO settings to a point, though exposures of thirty seconds or more can start to reveal a different type of noise in some cases. The long exposure time I get by using a combination of small apertures (larger f-stop numbers) does wonderful things to lights in the images, and makes the pedestrian walking through the scene disappear completely from the photograph.
These are reasons I often shoot like this at night. The main point I was trying to make earlier is not that you should shoot this way at night, but instead that it isn't necessary to seek the fastest shutter speed you can obtain to capture an image at night.
In the "Streets of Madrid" photo above (the next to last one in my first post in this thread), you'll notice some interesting things if you look closely at the photo.
I hope this has been helpful as you work to improve your skills.
