What Ive always done is to take the expenses paid by company to you (mileage & meals) as income on top of what they are paying you to do the job. (i.e. you are accounting for all money given to you through your business which is important to avoid any problems with the taxman at a later date!). I then process the same money that I have paid out as mileage/meals on my profit/loss statement as operating expense. (i.e. they are required for you to do the job).
This operating expense then comes directly off all the money you have received in (cost of sales) and you dont pay any tax on it. (i.e what you receive in for mileage/meals it is exactly what you've paid out for it with no profit earned). More importantly you have accounted for all your monies on your tax return. How the company handle the money they give you on their tax return is their concern, you have accounted for all monies you have received.
Not too sure how you handle the hotel bills as this could be considered a benefit you are receiving? Ive always pay my own and claim back, that way I know I havent received anything that could be construed as a financial advantage by the taxman in any way shape or form.
As Murdoch has stated, probably best to speak to the HMRC for a direct answer or better still speak to an accountant who may be able to give you some further pointers. And definately as Tel says, if you are handing in receipts then keep copies for your tax return to prove you've spent the money!
