I filed my 2013 income tax before April and got the refund by direct deposit to bank.

After that I applied ITIN for my daughter and with that I submitted my amended return manually in IRS office. I got the ITIN after talking to IRS and it looks like the address in W-7 was incorrect. I have yet to receive some refund based on my amended return.

So I want to know will I get a refund cheque this time from the IRS or they will do a direct deposit (just like they did first time)?

Not sure. Most amendment refunds are by check, but sometimes the IRS will do direct deposit on amendments filed in the same year.