What you have stated is correct. Section 138 attracts even if you issue stop payment instructions to your banker.
However, you can protect yourself by lodging a police complaint against the persons who extorted cheques from you and get it registered. This will be a prima facie record to you to establish that you have acted upon at the right time.
Even if the cheque is bounced because of stop payment, according to a supreme court version, if the bank account is having sufficient balance to meet the cheque amount, and if the person who gives stop payment is having valid and sufficient reasons for giving such instructions, the accused can be acquitted. This means that you have to establish during trial that there is no legally enforceable liability for the cheque taken by them and because of that reason only you have stopped the cheque from payment.