Sound is difficult to manipulate. It's hard to cut. And it is normally awful in a poor filmmaker's movie. How do you avoid this? Hire a professional. There are a million things to know about sound, and I know about five of them.
Since you and I do not have money to hire a professional, we must plow ahead as best we can.
Let's say that you got pretty good audio while shooting on set. If you didn't, you can try to bring your talant to your editing bay and sitck a mic (or your camera) in his face and have him try to re-dub his lines, but from my experience doing this has terrible results. If you didn't get good audio, either scrap your film, make it silent, or reshoot. The post alternatives are either too frustrating or too exacting to be of any use to people like me.
While cutting audio and video together, you must not be afraid to take audio from one take and put it under the video of another. Using "cut-aways" or close-ups to make this switch is the way to go. Basically, if you really like the talant's first part of a line from one take and the second part from another take, don't be afraid to combine them. "But it looks bad!" Not if you cut to another person listening to them or a close up of what your talant is doing for a moment and then come back to your talant.
Tiny audio "cross fades" (a couple of frames in lenth) are really helpful on cuts that "pop" or make some other horrible noise. Basically what causes these sounds is that the soundwave of your last clip is not quite in line with the sound wave you are coming into. For instance, the sound wave of the first clip may be at the top of its arc and the second clip may just be starting to go up. On the cut the computer has a wave that just drops off, which is translated into a "pop" or click. By doing a quick fade between the two clips, this sound is usually elliminated.
If you have a noticable "hiss" in the background of your audio track, you may notice it change between takes or go away and come back. Either add a very short audio fade between these shots, or take your "room noise" recording, and splice it behind the clean audio portions. By making the sound uniformally bad, it will actually sound better to the audience. If the hiss comes and goes, each time it comes back it will remind the audience that it is there.
As you build your soundtrack, include the sounds that you expect to hear and drop all the rest. If someone is walking down a hall, have the footsteps. But less is often more. Too much sound, and you loose the "audio image" and the sense of realism is lost, as odd as that sounds.
There are many things to know about EQing and other crazy things, but I know nothing about them. The bottom line is this: Does it sound good? If so, move on to
Authoring.