this has been discussed a number of times.
When your story settings don't match, you need to import story by story so you can correct vertical alignment.
Alternatively, you can save each building as a library part and place that.
This last can help you quickly site the buildings as all storys move as one.
Later when siting is set, you can do the single story hotlink.
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"