Here is an example (chart of accounts is balancing-natural account-intercompany)
I define the following rule
|Debit BSV||Credit BSV||Debit Account||Credit Account|
|All Other||All Other||99-4000-99||99-2000-99|
Then I enter a journal
When I post this, the balancing lines generated are
So you can see we discard the BSV and Intercompany segment from the set up and use the correct ones from the transactions. If we always reatined 99, we would be using 99 as a clearing company for everything, if you wanted to do that you would use the clearing company options.