A car allowance (unless it's in the form of an Employee Ownership Scheme) is just an additional to your salary, and as a result you pay tax and NIC on it. If the addition is sufficient to take you into a higer tax bracket, then you'll pay higer-rate tax on the amount over the threshold.
As to what to do with it, that's really up to you. Be aware, however, that if you are expected to use your car for business (as opposed to a 'perk'), then the increasing emphasis on issues such as Corporate Manslaughter mean that your employer may wish to place restrictions on the type of car, age, mileage and so on, in order to have some element of control over its business drivers. It's for this kind of reason that many employers are moving away from the cash allowance, and back to providing cars for employees. There's more admin for them (which is whay they went to cash allowances in the first place), but the risks are lower and more easily controlled.
If you have complete freedom with regard to the car, then do as you wish. Use the money to pay for a loan, a lease, or PCP, whatever. Keep some back for repairs, insurance etc.
Don't, however,treat it as just extra money in the bank each month. If, for example, your employer decides to revert to the managed-fleet solution, or you change to a job which doesn't give a car allowance, then you'll take a hit in your monthly 'disposable income'
PJ
PS: Having paid tax and NIC on the allowance, there are no real gains to be had by playing smart in any way. Your employer will presumably pay you a rate per mile for business mileage, and that can be up to 45p per mile for the first 10,000 miles, and 20p thereafter before you suffer a further tax liability. These rates are set by the Inland Revenue, and are intended to cover RFL, insurance, fuel, repairs, maintenance and so on, so if you do get paid a rate per mile, then you probably wont be able to claim any further costs from your emploeyer without having to pay tax (unless they have a dispensation with HMRC, which is unlikely)