Although all planes are different, I usually apply my flaps right before I turn into my final approch (while still at 90 degrees to the runway).

As for lining up your approaches - before you fly, walk out onto the runway and line up a reference point parallel to the centerline fo the runway. You will be surprised! From the flight line, you will see what I mean. If you don't do this, your turn into final will often occur way too soon. I used to make this mistake on new fields all the time. From where flight lines are are, it's hard to guage a reference point that lines up with the centerline of the runway without actually walking out there and taking a look. Try it, I'm sure it will help.

Best of luck.