Yes, it sounds like there is a direct nexus between the 1065 and the 1040.  You will have to determine if there is.  

So, if the 1065 is paying rent to the 1040 [and LLC issued a 1099 to the 1040] report the rent income on 1040, Sch E, line 3 and the same amount as expense on line 19 labeled "To Sch F, line 7".  The Sch E will net to zero.  Report the rent on Sch F, line 7 and all other expenses on Sch F.