Holiday and other types of contractual rights are tough to pay when you are a small business arn't they? You used to be able to pay holiday pay on a weekly basis but not any longer as you say.
What I do is to keep a seperate desposit account for all the expected vat and other non regular expense bills and pay over a regular amount each week into them. This stops the shock of having to find money for the extra bills that come in. The best way to do it of course is to open up an instant access account with the highest savings rate you can find and stash an amount in there until you come to need it. And yes, I would put an amount by for tax and ni as well.
Hope this has helped somewhat.
Cheers
Sue