There is no system in place, and ebay does nit seem in any hurry to fix it.
Either you pay in total and seller refunds excess or seller cancels all sales and relists as one item.
Serious problem for sellers with simple postage, if three items are put in a package together, there is only a tracking number for one and two items are untracked, leaving seller open to claims of not received.
In the days when postage was really easy, same tracking number could be loaded for all item, but now printing the label automatically loads for just the item the label relates to.