It’s entirely up to you. Even though you may issue supplementary cards to employees, they should only be using them for expenses related to your business, not for personal use. (You will need to have strict company rules in place to ensure this.)
Since it’s your business, you may decide to keep for your personal use any rewards points generated by supplementary cardholders. But be aware that an excessive number of points (250,000+) earned by a business card in any one year may attract the notice of the tax man. In this case the safest thing to do is to convert the rewards points into a cash offset against the card account, if this option is available, thus reducing business expenses rather than getting a personal gain. Another possibility is to utilise the accumulated points to reduce business expenses by using them for business travel or to purchase company assets.
Alternatively, you may decide to let your employees keep the rewards points themselves. In this case it becomes a worthwhile staff incentive, and it shouldn’t have any FBT implications unless it is obvious that most of the expenses of the business are deliberately being directed through a particular employee’s card in order to create an incentive.