Josh,
Try setting up the different systems as hotlinks. For example, the building skin that you are working can be hotlinked back into the main file. Since you started that file from an older version, the skin should be correctly aligned with the rest of the building.
Using hot-linked files is tremendously easy and facilitates work flow. It can be used in conjunction with Teamwork (when you get there).
As for placing the Interior Elevation Markers, without teamwork, you might have to schedule working in the main file to place them. You need to place the extents of each interior elevation. You could copying the latest floor plan file, place the IE and then copy/paste them into the main file. This would save you some time.
This may lead to a discussion about differences in work assignments and work flow for this [new to your office] CAD.
Teamwork is really quite easy to set up and use when you are ready.
Erika
Architect, Consultant
MacBook Pro Retina, 15-inch Yosemite 2.8 GHz Intel Core i7 16 GB 1600 MHz DDR3
Mac OSX 10.11.1
AC5-18
Onuma System
"Implementing Successful Building Information Modeling"