One off fee usually. It is not unusual for the fee to be 3 to 4 times the nannies weekly salary.
You don't need to us an agency though, you could recruit yourself using websites like NannyJob and Childcare.co.uk but you would then be the one to sort through the applications and decide who to interview.
An agency should help you through the process and will be able to CRB check any applicants who don't already have a CRB check (though nannies who are on the Childcare Register won't need an additional check as Ofsted get's updates).
Make sure you agree a Gross salary, as a nanny working 3 days per week could well have another job. A good agency will tell you that, not so good agencies seem to still think we are in the Victorian times and deal in Net wages! You can tell this is a pet hate of mine... nannies are like any other employee.
If you have plenty of time, you could try self recruiting first... then if you don't get anywhere you could then use an agency. You will find a lot of info on here about recruiting a nanny. We often have discussions about nanny contracts, nannies duties, payroll companies and taxation.
A good agency may well find you a great nanny. A not so good agency may just send you a load of CVs - you can get that for a lot less using the web.
Consider what it is that you are wanting the agency to do, then check with them that they do that and what it costs. Then it's case of if you feel that is worth the money they want to charge.