"Aufwachen" and "wache auf" are indeed the same. "Aufwachen" is a separable verb. It depends on the sentence which one you can use:

Ich wache jeden Morgen um 6 Uhr auf. - I wake up every morning at 6 o'clock.

Ich muss jeden Morgen um 6 Uhr aufwachen. - I have to wake up every morning at 6 o'clock.

Here are some links but you can also google for separable german verbs if you need more

http://www.jabbalab.com/blog/984/german-separable-verbs-and-verbs-prefixes

http://www.vistawide.com/german/grammar/german_verbs03.htm