It seems that the content network has a lower CTR than advertising just strictly through Google Search and their Search Network. Does your CTR in the content network affect your CPC for Google Search and the Search Network?
No, they're all considered separately. https://adwords.google.com/support/bin/answer.py?answer=21388 https://adwords.google.com/support/bin/answer.py?answer=10215&query=ctr&topic=&type=f&onClick=
even when your keywords go to "poor" in search you can do quite well on content network and vice versa.