The BALPA negotiated allowance is really for employed pilots. Self employed is a bit more complex. If you use your home as your base, you can claim for mileage to the airport, any hotel costs which are not paid for by the company you are working for, any other commuting costs (train, bus, airfares etc.), meals while away from home (again if not provided), incidentals like telephone calls and so on. Medicals and any CAA licence costs as well.
The thing is to keep receipts for everything and keep a log of everything you spend. It makes it a lot easier when doing your accounts at the end of the tax year. Also consider paying self employed NI.
I personally use a reputable accountant. It is obviously an added cost but even that cost is tax deductable. They can keep you right as to what you can claim and what you can't and also HMRC are more likely to accept your figures when coming through an accountant. Otherwise you may find them asking questions or investigating you even if everything is above board.
Also don't forget to register with HMRC as self employed.
But as Kiltie says, nothing to stop you doing it yourself.
Good Luck