Firstly you list FAB/EGLF as your base? If you are FAR91 irrespective of where you are based, you still have to apply IRS applications. This is one heck of a hell hole. The only way to go is to consult your corporate tax lawyers who can gain superb assistance from the tax specialists at NBAA in DC. I doubt if you are not a NBAA member, so use the folks in DC, they hold tax seminars around the US.
Charging from Flt Dept to individuals and/or depts within an organization is a normal practice.
Good luck & enjoy FAB this summer.
Check
www.NBAA.org, if not a member JOIN TODAY