They will send you a notice to submit the cheque for $50.00.
I paid by personal cheque, got no problem with it. I don't know about merlion but if you read in the instruction in the forms, they accept personal cheque. Just make sure you have money in the bank. Its easy with BCIS, you don't pay it correctly, they won't process it.
I also traced my 13 numbers from my returned personal cheque from the bank before BCIS sent me the NOA.