I think you're getting confused.
"visa4uk" is the official UKVI online visa application website for applicants oustside of UK.
(ie Philippines)
You need to register an account and submit the application online then a print-off taken and submitted at the application centre
The online application you submit is pretty much the Personal Details form VAF4A
The visa fee must also be paid online.
The Appendix 2 needs to be printed and completed by hand and submitted at the application centre together with VAF4A print-off and all other supporting douments.
Does that help ?
Sorry if my explanation is not so clear.