This is a pretty popular question. Many brides opt to wear heels for most of the wedding ceremony, photos, and into the reception. However, they anticipate that later, they will need or want to change to more comfortable flats. The big concern for many is- sometimes that is a difference of several inches between two different pairs of shoes- so what to do about the dress length?
A popular choice is to plan your footwear based around time of bustle. You should plan on wearing the shoes you plan to wear to your ceremony at your fittings. Have the alterations done to echo that shoe. When you attend your fitting to create the bustle- bring the shoes you plan on wearing later on (if they are of a different height)- and alert your seamstress so she can help pull the dress up a bit to accommodate for a smaller heel.
Another choice is to go mid-range in your footwear selections and select a medium heel for both pairs to wear at ceremony and reception!
Of course, another option is to find a pair of shoes that are a comfortable height to last you the entire day and night!