I’d say you have made an understandable but fundamental error with regards layers.
Do not asign raw geometry to layers, only groups and components.
Read up on layers in the help section.
@Box is correct. While it is indeed possible to assign raw geometry to a layer and in some very specific circumstances you may want to, you are better off making things into groups or components before assigning it to a layer.
Next, as @DaveR requested, please post the model so we can take a look at it. Screenshots are a great start and if that is all you can post for some reason I can still work with you on this but having access to the .skp file is always my preference.
Finally, in response to your question, I prefer to create my models one section at a time. I try to plan out where one section of my model will end and another will start before I get too far in to the modeling process. By planning ahead, you can keep your layers clean and avoid this sort of problem.
If you need to fix this, it may just be a simple case of moving a few things from one layer to another but I can not say for sure without actually getting some more info about your model.
Ok, I looked at your model and if I understood your question correctly you want to have the building sides that are part of your basement layer to be part of you building layer. That would just be a process of moving them from one layer to another. However, this will create holes in the basement layer. If that is ok with you then I can walk you through how to do it. If you are not ok with holes in the basement layer then we can be a bit creative and create a new layer for the walls that can be displayed alongside the other layers. If you are planning on adding textures later, this would be the method I would recommend.
Let me know how you wish to proceed and I will be ready to help.