It doesn't need to be separated out on the P60.
What usually happens is that a percentage of the flight pay is taxable. This percentage is then taxed under normal PAYE rules at your highest marginal rate of tax.
Your pay in this employment box will include the taxable flight pay ( normally) and the adjoining tax deducted box will show the total tax deducted including that element applied to flight pay.
As a result you don't to complicate matters by showing it anywhere else on the return.
Other benefits in kind such as loss of licence insurance or private medical care or subsidised company loans etc are taxable and will not usually have had the tax deducted so you do need to declare these seperatley at boxes 1.12 to 1.23.
Hope this helps.