I seem to recall that I couldn't pay on line at the time. So we had no choice. I filled the application forms out online on both our behalves. My recollection is that my wife had to go to a bank of their specification (BDO) with her printed "ticket" issued by the NSO upon application, which she had to take with her, along with the money, to the bank. It was only a matter of days / less than a week between applying for the CENOMAR, paying the fee and my wife receiving both CENOMARs through the post.
At the time we applied for the CENOMARs it was about 2 months ahead of the wedding. Worked okay at the time.
I genuinely dont know if going direct to the NSO would be any quicker / better.