You can! If you schedule an appointment on the client's behalf and want to apply that appointment towards a client's existing package that's totally doable.
All packages clients have purchased through your store can be seen in the View Orders page of your account; in that page click on the client's package you'd like to apply towards their appointment, then copy their code.
During scheduling click the arrow icon next to the "Forms, Codes, and Notes" area, and from there you can add your code into the "Coupon or Package Code" field.
Once a package code has been successfully applied to an appointment that appointment will be removed from the client's remaining appointments on their package.
You can also edit a package code into an appointment after it's been booked. To do this, click on the appointment from your calendar and click the "Edit" button in the appointment toolbar. From there just edit the code into the "Code" field, save your changes, and you'll be set!