Run the deposit process to create all of the deposits from the Sales revenue sources.  Payments will not be available to post to the General Ledger until they are included (linked) in deposits.

As long as you've got both pieces of the transaction (the Sales Orders and the Payments) everything should balance out in the General Ledger when you attempt to post again.

If you already posted just the Sales Orders then, you can post the Deposits separately just by running the post process again for the same dates.  This will result in two output files which can either be merged in Excel or imported separately but the GL details transactions contained will be exactly the same.