By using this website, you agree to our Terms of Use (click here)
The Ship Separately and Bill Separately settings on the Order Types (SO201000) screen control whether or not Shipments and Invoices get consolidated.
First, a minor gripe about how the Ship Separately and Bill Separately settings are listed on the Order Types (SO201000) screen. Ship Separately is listed second even though Shipping comes before Billing. Maybe Acumatica can fix that in future versions 🙂

Ok, now that we have that out of the way, back to the point of this post.
The Ship Separately setting is easily understood. If you check this box, Acumatica will generate a separate Shipment for each Order instead of creating one Shipment across more than one Order for the same Customer.
No problem there.
Now, for the Bill Separately setting. This setting is easily misunderstood.
Some people interpret Bill Separately to mean this: Each Shipment will get a separate Invoice.
What Bill Separately actually means is this: Each Order will get a separate Invoice.
The Help in Acumatica does point this out, but you have to read it carefully

Now, many people would never even notice that their understanding of Bill Separately is incorrect. Why?
Let’s say that you are generating invoices daily. As long as you only generate one Shipment for each Order in a given day, then you would never notice a problem. Bill Separately only becomes a problem when there is more than one Shipment against an Order during a day. This is unlikely to happen, but it is possible.
Of course, if you are generating invoices weekly or monthly, then you are more likely to notice a problem.
For those who are more visually oriented, here is how some people think the Bill Separately setting works (both checked and unchecked):


But this is how the Bill Separately setting actually works (both checked and unchecked):


The only way I know of to truly guarantee a separate Invoice for every Shipment is to use the Automation Steps screen to automatically prepare the Invoice as soon as a Shipment is confirmed.
