When we encountered the unfiltered nature of the data for the first time in IM, we added a SEQUENCE number (Counter Column) to that data. So, when the Invoice number changed, the counter resets to 1. We also made sure that the account number on line one was the AR or AP control and therefore the account that should represent the full amount of the transaction. In this case ALL invoice headers are filtered by the number 1. So your header would only have 1's in that column. Why I mention this is that in 'filtering' the header for the single line works, you do not want to filter the 'detail' - as the header line is in fact really just another line of distribution.
As noted by Richard, as long as you are sorting and linking on the Invoice Number you should not have any issues. Remember that if you sort and group the header on one column or the other, then you will want to be sure to sort the detail on the same column - makes it easier to read on screen. Regardless of sorting, the linking ( I believe ) is the key to the integration.
