Steve,
As you already know spouses of Filipino citizens can stay in the Philippines for 12 months under the visa free Balikbayan scheme then renew again by exiting and re-entering etc.

Well I have decided to take the alternative route and apply for 13a perm residence right away.
So I need to comply with the current regulations so that my wife can submit a compliant application when we are actually there.

The needed documents have to be 'legalised' by the Philippine Embassy before Philippine Immigration will accept them.

The process for legalisation varies slightly depending on the specific document.

Police Clearance Certificate from UK is needed.
This then needs to be certified by a notary public.
Then it needs to be legalised by the UK Foreign & Commonwealth Office.
Then it needs to be legalised by the Philippine Embassy

UK marriage certificate is already a certified copy of a register entry so this can be legalised by the FCO without needing attention of a notary.
This also needs to be legalised by the Phil Embassy.

Then I need proof of income which apparently also needs to be certified.

As I said, we've decided to apply in Philippines.
It's also possible to apply here in UK at the Philippine Embassy.
Here's the application form for Philippine Embassy

Here's the application form for Philippine Embassy

I'll post the form I'll be using in the Phils when I have a better connection.
Hope it helps.

You'll need the Police Certificate, marriage certificate and proof of income in both cases.