Well manual check entries could have a vendor number, but I assume from the information you provided that you are doing miscellaneous Cash Invoices for vendors not on file. In this case you are correct that an Adjustment batch is not the necessary function to reverse checks.
The correct way would be to go into Check Reconciliation and instead of Clearing the check, you should Reverse it. This will generate all the necessary transactions to send to your general ledger in addition to allow removal of that check from the system.
Typically you would want to do Reversals from Check rec, even for vendors on file, because this process 'un-pays' invoices, unlike using an Adjustment batch where you have to be extra careful that you are doing the reversal in the proper direction and are hitting all necessary transactions.