When I applied for the tourist visa. I paid at Standard Chartered Main Office in Makati and they know all what to do and they'll instruct you and guide you through the process. Know hassle. It was quick!
When we applied for the spouse visa, we paid through Metro Bank at a branch nearest to my home. They don't seem too organize as the Standard Chartered people, but they know what to do. You'll have to fill-up the payment bill form and payee should be British Embassy Manila. But you have to know the exact fee as the Metrobank tellers don't know this. Also photocopy a passport page as this will be attached to the form for their file.
Apparently, during that time, I forgot how much is the exact fee but I know it's less that P44,000. But nevertheless, we paid exactly P44,000. Upon submission of the requirements at the VFS global. The staff there said the fees was increased, so I was asked to pay an additional of P3,000+ (as far as I can remember) right there and then and gave me a receipt.
VFS global said, it's all good.
Hope that helps. =)