Related Questions:
How do I control which menu items are shown on my different documents?
How can I have different versions of proposals on the same booking?
Answer:
To create multiple Documents with different Menu Items on the same booking you will need to create separate Events or separate Invoices on the Booking so that the Documents can pull in the correct batch of Menu Items.
Events
Create new Events to associate your different batches of Menu Items to. Once a selection of Menu Items has been approved you can delete the Event you no longer need.
Invoices
Create Invoices to hold your different batches of Menu Items. When creating the Invoice be sure to select the "Invoice" option if given.
Once you have set up your different batches of Menu Items you can pull those into your document by editing the Menu Item Document Element and selecting the Menu Item Source. After making any changes click Apply.