If you are self-employed your flat rate expenses should be declared as income, and then you should claim a tax deduction for the actual travel costs incurred (if using a car, need to keep detailed records to claim this).
If you are PAYE, again you will be taxed on flat rate expenses paid (I assume round sum allowances rather than Revenue limits), and you can then claim the expenses incurred based on Revenue limits if using a car, or actual expenses incurred.
What expenses are you paying?
What expenses will you incur other than travel?