I would start out by organizing the Flask app in the standard structure as follows:
app
|-- app.py
|-- static
|-- css
|-- img
|-- js
|-- templates
And as btford mentioned, if you are doing an Angular app, you'll want to focus on using Angular client-side templates and stay away from server-side templates. Using render_template('index.html') will cause Flask to interpret your angular templates as jinja templates, so they won't render correctly. Instead, you'll want to do the following:
@app.route("/")
def index():
return send_file('templates/index.html')
Note that using send_file() means that the files will be cached, so you might want to use make_response() instead, at least for development:
return make_response(open('templates/index.html').read())
Afterwards, build out the AngularJS part of your app, modifying the app structure so that it looks like this:
app
|-- app.py
|-- static
|-- css
|-- img
|-- js
|-- app.js, controllers.js, etc.
|-- lib
|-- angular
|-- angular.js, etc.
|-- partials
|-- templates
|-- index.html
Make sure your index.html includes AngularJS, as well as any other files:
<script src="static/lib/angular/angular.js"></script>
At this point, you haven't yet constructed your RESTful API, so you can have your js controllers return predefined sample data (only a temporary setup). When you're ready, implement the RESTful API and hook it up to your angular app with angular-resource.js.
EDIT: I put together an app template that, though a little more complex that what I've described above, illustrates how one could build an app with AngularJS + Flask, complete with communication between AngularJS and a simple Flask API. Here it is if you want to check it out: https://github.com/rxl/angular-flask