it applies as follows:
whole house from the footprint and overall shapes;
house floor by floor individually (so those being different doesn't matter); and
each room individually.
You can even so specific spaces, such as your desk space, your furnishings in a given room, etc, using the bagua.
But, i recommend this:
start by decluttering;
then do a space/energetic cleansing;
then do the furniture/ornament placements.
if you do the ornament/etc placing first, it won't have that much of an effect. but if you cleanse the space and then do the ornaments/placing, you'll be in good shape.
if you don't yet have time to declutter, use the bagua as a "decoder ring" for what is going on in you, your house, and your family. if you do it by house footprint, then by floor, then by room, you can see how certain areas of your life are affected. That is to say, if the relationship corner in every room, every floor, and over the whole house is cluttered, or has broken objects, or oddly shaped, or what have you, this might also be why there are relationship problems in your life. (not saying this is the case, just saying that it can 'show' you things).
then, by going through the process of decluttering, cleansing, and then bringing in the remedial fixes, you'll really see things soar.