This all comes down to the specifics of your employer's travel policy and its flexibility. Even when one must book through a corporate TA, a growing number of employers have made arrangements for employees who wish to do so, to provide a personal credit card. The allowable amount is billed to the employer and the balance to the employee. An invoice is then generated which shows the breakdown and an explanatory note is added.

Yet others simply allow employees to book their preference but require that the entire cost is charged to a personal card and then the reimburseable amount reimbursed.

The larger issues are that there are many employers who book fully flexible fares. If an upgrade is to an inflexible fare, it may be cheap but does not meet the employer's needs. In that case, you may be stuck with the entire cost of the ticket if a change needs to be made.

The real key is to sit down and have a thorough discussion. There are some employers who are thoroughly rooted in the past and others who see flexibility as a relatively cost-free way of keeping employees happy.