I've seen this done a number of ways.
The more automated way is that the feed from the Advancement system to the general ledger creates two transactions for the one donor gift, transmitting the charitable portion to a gift account/object and the non-charitable portion to a different account/object code. As John said, the non-charitable portion of the gift might be fed to a different "object code" or "natural" in the same account, or fed to a different non-gift account altogether. The transaction wasn't necessarily split on the Advancement side; if the Advancement recording is the full amount as the "gift amount" and there are benefit/premium codes/amounts associated with the gift-system transaction, the gift feed can be written to adjust the amount of the gift portion and create a separate transaction for the benefit/non-deductible amount.
The less automated way was that the entire amount was transmitted to the gift account/object, and then a later report was run to adjust money from the gift account/object to a different account/object using a journal entry. Sometimes that report created a batch to make the actual adjustment journal entry transactions directly, but alternatively the report was used in the Finance office to manually enter adjustment journal entries. From an accounting point of view, whether the separation of the two parts of the transaction happened at the time that the gift was transmitted to the general ledger or happened at a designated later time (monthly, or even at the end of the fiscal year) wasn't considered material. Generally, there would be one cumulative journal entry for every gift fund that included such transactions (so, possibly, one cumulative journal transaction for all gifts to the corporate partners program, or one cumulative journal transaction for each fund-raising event), so it wasn't a heavy lift for the Finance office. It worked pretty well, even if having it all happen automatically during the initial transmittal is more satisfying/elegant!
My US$0.02 worth; the usual disclaimers apply.
Good luck!
Alan
Alan S. Hejnal
Data Quality Manager
Smithsonian Institution - Office of Advancement
600 Maryland Ave SW Ste 600E
PO Box 37012, MRC 527
Washington, DC 20013-7012
Voice: 202-633-8754 | Email: HejnalA@si.edu