More often than not, each level will have a different flow of energy as defined by its floor plan, so start with the main level bagua and then proceed to the next level.
The feng shui energy flow in the whole house is greatly influenced by the energy of the main floor, so it is always wise to do your best with the bagua of the main floor first.
To define the bagua of the second floor, work with the same direction of the front door (you can even superimpose the second floor bagua over the first floor bagua according to the house layout, just to make it easier for yourself.)
These feng shui videos and tips will help you further:
How To Take The Compass Reading
How To Define Your Bagua: Free Video Tip
All About Your Home Bagua: Feng Shui Tips and Solutions
If you find you have any missing bagua areas, these tips should help:
Feng Shui Guide to Dealing with the Bagua Missing Areas