Stock transfer in feature, only available for multi-sites store, is used to accept a stock transfer from another site. From a workflow perspective a stock transfer follows the corresponding stock transfer out. 

In respect to the general ledger postings, there is a Stock Transfer Contra Account. 
When transferring from stock from one site to another site, the stock on hand general ledger account is affected but the other side is the stock transfer account.
At some point in time, the stock transfer out needs to be reconciled and a journal entry will need to be inserted to balance it out.