each property should be in a separate column on schedule E. if the mortgage relates to multiple properties you'll have to allocate. if you don't you will be creating problems if you dispose of one or more but not all in one tax year. you may also need to do this to comply with passive activity rules.
from IRS instructions for Schedule E
General Instructions for
Lines 5 Through 21
Enter your rental and royalty expenses
for each property in the appropriate column
