When recording, make sure the tape is rolling and that you're not in pause mode. Don't use the pause button. About 5-6 inches is good, the length of your outstretched hand. If it's any farther away you will still be able to hear what people say, but the recording will lose its power and intimacy. You will use these sounds later when you produce the story.
Long pauses are okay.
Umms are okay. Saying stupid and embarrassing things is okay. Often the stuff you think is weird, worthless, or that you initially want to edit out, will end up being the best and most surprising parts of the story.