[OokieWonderslug (OP)]

In every reconstruction I have seen the Atlas mountains do not match up with the Appalachians at all. There should be a line of mountains on the west coast of Africa, yet there are none there at all. It is perfectly flat. How did Africa collide with America and not leave a line of mountains on both sides? What am I missing here?

It would be logical to think the Atlas were made by Africa smashing into Europe. They are in the right place and the area is in the process of colliding. If the African side eroded away, why are there still mountains in America when it has always had more rain and would seemingly have eroded away much faster than Africa?

What am I missing here?

[Mazurka]

On one hand you are right - the modern atlas mountains were formed in the first half of the cenozoic era as Africa and Europe collided. 

What you are missing is how these mountains formed.  The Atlas mountians are formed from Mesozoic sedimentary rocks, uplifted during the collision of Africa and Europe.  The sediments were derived fromthe Anti Atlas mountains that were formed during the tail end of the Caledonian Orogeny - which is sometimes called the Appalacian or Alleghenian orogeny.

As I have said before there are truly incomprehensible periods of time involved with all of these geological events and a lot can happen in that period of time.  Rates of uplift/ erosion driven by other tectonic events as well as changes in claimte paterns due to the locations of oceans and atmosphere composition.

If you are really interested a few good search term to start with include: Caledonian Orogeny; Appalacian Orogeny; Alleghenain Orogent (which are broadly the same thing).  Hope this helps