You should always look at your main character's fatal flaw as the major building block of your story. And, as such, it is her flaw that should inform every scene of your story.
First and foremost, you need to make sure you are not writing what your main character's flaw is in a "tell-tell" fashion. You need to be showing HOW her flaw manifests itself as an obstacle in her life. You need to establish this flaw in the first pages of your story. Then, throughout the course of the story, this flaw needs to be revisited constantly. What I mean by this is that if your main character's flaw is that she is too submissive with her husband, for example, then it's your job to brainstorm ways in which to show her not standing up for herself -- and we need to see this throughout the story. Then, at the end of your story, she needs to be getting over this misbehavior in some fashion -- unless your story is a tragedy. (In tragedies, the main character never gets over their flaw.) Or if you main character suffers from, for example, commitment phobia -- as many do in romantic comedies -- then you need to brainstorm scenes in which this is happening and place them throughout the story. Of course, as the story progresses, she should be overcoming this flaw, only to revert back to it at the low point (e.g. the "all is lost" moment). Ultimately, however, she needs to get over the flaw at the end. Christopher Vogel asks us to think of flaw as an addiction. Often times people must relapse into their bad habits before they are able to really put them behind them for good. But back to flaw... If you story is a comedy, then these flaws need to manifest in humorous ways. If it's a drama, then the flaw needs to create pathos or suspense. You get the idea.