What kind of camera do you have ?
Normally in
Auto mode your camera makes just about all the decisions for you. You don't have to worry about the various exposure modes, just point and shoot. Most of the time it does a pretty good job, even if the results are a little less than artistic.
The various
Program modes allows you to be creative by allowing you to have control over the flash, shutter and lens; just to name a few.
In response to your question, I would normally say there is no carry over effect, but I want to check your camera model first.