In order to import lookup fields you need to render the CSV source attribute in the following format:
" [ Related Entity Type Name ] , [ Related Entity Instance GUID ] "
For example
"account,{BB51BC3D-98EB-DC11-9C73-0002B3C73EB0}"
Here is a complete contacts.csv example
FirstName,LastName,ParentCustomer
Adi,Katz,"account,{BB51BC3D-98EB-DC11-9C73-0002B3C73EB0}"
Notice the " " wrapping the lookup value. This is because a comma (,) is used to separate the Related Entity type and value.