The approval process can take several months, so allow for some delay (at least 2 months I would say). The scheme does change in April this year (2007), when Ofsted start taking it over. However, if your nanny becomes approved under the SureStart scheme over the next few months, they will remain on the SureStart scheme, and transfer to the Ofsted scheme when their approval is renewed. I think that SureStart Childcare Approval Scheme is not accepting new applications from September 2007. Ofsted should accept applications from April 2007 - though no paperwork details on that yet.
With regard to Nanny PAYE, you do all the usual HMRC paperwork as per usual. Once you get to the point of producing the payslip, you will have the NET PAY DUE figure which you pay to your nanny. From that NET PAY DUE figure, you then deduct the voucher payment amount, so the nanny gets their NET PAY DUE in two chunks... the voucher, and the remainder via your usual pay method (BACS/cheque/cash).
As employer you therefore do not save anything off your employers NI payment and the nanny has to pay Tax and NI on their gross income as per usual (employer deducts Tax and NI on employees behalf).
My employer uses a voucher company called FairCare, which pays me electronically and works really well. I would suggest opting for electronic vouchers where possible, makes it easier for most people I would have thought.