I am sort of annoyed at this question, since it's mostly self evident. I think you have to come from a position of arrogance to assume it wouldn't affect us negatively. But since you and Coach and a few others seem adamant, I will give you my take.
First of all - Manning's body is unique after 4 surgeries. There are throws he can make, throws he can't and limitations that are specific to him... He certainly would have disclosed all of those weaknesses to McCoy throughout the year as they gameplanned. So that's the biggest thing - he knows Manning inside and out.
He also knows what Manning likes to do in almost all situations because they obviously discussed preferences, strengths/weaknesses as they gameplanned. e.g. Does Manning prefer comebacks on 3rd down with a certain set of variables that aren't evident on film? He knows the logic behind calling certain plays at certain times.
He also knows how we like to attack the current Chargers roster.
Plus - the offense is actually pretty simple -
http://www.grantland.com/story/_/id/...denver-broncos - so it's not like a Shanahan style offense that completely changed from week to week. It's fairly static, and arguably easier to pick out nuances that would help a team defend against it.