Hello

when you buy a ticket from a 3rd party vendor you normally/usually cant modify all aspects of your booking directly with airline until take off (or the moment you checkin i am not 100% sure ) , so you need to ask amex to do it on your behalf and the cost will be paid later

You can do basic stuffs like changing seat , adding luggage and so on.....

If your company is efficient and accounting is not a pain in the @$$ , they can allow you to make such requests and then you will pay them back later . Otherwise try to upgrade during checkin , this can be done directly with airline and won't involve amex and your company

what was the configuration of your last flight ? same airline ?? also what did you changed last time ??