I checked and our policy doesn't address this.. I would put it as a separate airline line item expense and see what happens.. right now till its addressed I think they would look at each charge and determine from there

ie.. bags.. they would pay
.. preferred seating like NW and their $15 aisle seat charge.. probably not

I think all companies will have to address this sooner than later though

Now on that note.. as with any change.. you can always turn the rules to work for you.. in my case.. I'll really push to allow my company to do ALL flying on AA to keep elite status as it will have advantages of missing many of the fees