Maintain PDF transparency when importing and exporting.

My organization requires that we have a set of maps for our campus, some basic, some more detailed and specific to a department need. I was hoping to upload a blank map and additional PDF layers of resources from Illustrator so that if one team needed a specific type of resource, i.e. emergency related, or another team just needed one with labeled common spaces, that they could show/hide each layer as they need it. As it stands now, importing a transparent PDF that has been created in Adobe Illustrator imports with a white background. I prefer PDF over PNG to keep vectors scalable and transparent. I’d hope to do this for a few icons I’d like to import, too.