where specifically in the query should i use the Collate function?
I already have it in the middle part of the query.
Anywhere you're comparing or joining between the 2 databases. Think of it like converting 1 collation to the other. So if DB_A is Collation_A, and DB_B is Collation_B then your code will be:
select DB_A.dbo.TableA, DB_B.dbo.TableB
from DB_A.dbo.tableA TbA
join DB_B.dbo.tableB TbB on TbA.FldA collate Collation_B = TbB.FldB
That converts FldA to B's collation