Can we enter the INTERCOMPANY segment manually on a GL Journal Line Distribution?

Summary: Can we enter the INTERCOMPANY segment manually on a GL Journal Line Distribution? What are the cons?

Content (please ensure you mask any confidential information):

1. We have setup intercompany balancing rules - Chart of Account Rules - using Due to/Due From natural accounts? There probably was a metalink note or user guide, which says it is not a good idea to populate the Intercompany segment manually. Is this true?
2. The intercompany balancing lines (Lines 3 and 4) are still created when I populate the Intercompany segment on Lines 1 and 2 (Debit and Credit). Is this okay to do?

Reason : We want to use the lines 1 and 2 of the GL Journal to create elimination rules to eliminate revenues and expenses account from the Line 1 and Line 2. And having both company and Intercompany segment will help in filtering the intercompany transactions and build the rules. We cannot do these rules on Lines 3 and 4 (system generated lines) because the natural accounts are constant (Due To/Due From) and not the "real" revenue and expense account used on the originating journal.