First, there is no one proper way to use commas; however, there are ways to misuse them. It's confusing, I know.
Start by reading Strunk & White's
Elements of Style. It's not necessarily the be-all and end-all, but it's simple, straightforward, and thin.
[edit]I
had a friend
who would edit all of my letters, important e
-mail, and
, during college
, my papers.[/edit]
EDIT: For the record, your issue with commas in your OP is about whether or not to use the serial/Oxford comma (the last comma in a list). It's a stylistic choice. I prefer to use it.