You will be directed to pay the NHS surcharge once you have completed and submitted the online application.

So:

1) complete online application
2) Before submitting online check for errors or omissions as once you submit you cant change anything
3) Submit. you are then taken to the website to pay the NHS surcharge - pay and make a note of the IHS number
4) you are then directed back to the VFS site to pay the visa application fee. then you can select if you want to use a VIP lounge for which there is an additional fee. Pay for the visa application and select an appointment date.

The application wont be complete till all payments are made. then you can print out the online application. The your wife turns up at the VAC (visa application centre on the day of the appointment with the printed online application and all the other documents (evidence, TB certificate and IELTS)

If you wish to use Cebu to submit your application there is an additional fee. Not for Manila.