Hi Jason,
Actually, some of what you are looking for can be automated. When a sales rep creates a sales order, you can put actions on the save button that also creates an activity for the Accountant and even email them the activity notification.
Then, when an invoice is paid, you can also create another activity for Shipping to box the item, and again, send an email notification of that activity. For the tracking number, my advice would be to create a custom field or alternatively, use the ShipAddressNote field already available for invoices.
You would need to copy and edit the stock invoice screen to add both the field and the actions and replace the current stock screen. You would also need to change the ContactsPortal_Transactions screen to include the field for the tracking number.
I recommend copying and editing the CRM_NewActivity screen and editing the Save button. They action for creating a follow up activity are around Action #52. You can use these actions as a reference when designing you actions on the QuickBooks_SalesOrder and QuickBooks_Invoice screens.
Hope this helps,
Adam