There should not be any problem. All that matters is you should have a valid OBC-NCL certificate at the time of document verification and counselling. So even if you have filled the form first and then applied for a OBC-NCL certificate, as long as it is valid, there should not be any issue. This is because while giving you a OBC-NCL certificate, they assess the last 3 years of your finances. And so it is fine whatever time you take the OBC-NCL certificate.