So I figured out that a scenario step will roll back if there are any errors. To fix this I did the following:
1. Create Scenario Step for reading in the file and for each order, I place the order on a queue.
2. Create a second Scenario Step to be triggered by the queue and add the Sales Order. If there is an error, then it writes to the Messages/Alerts window.
File2Queue
I used the for-each (branch, split-join, xform) so that the receiver information makes it to the end of the process flow. Otherwise you have to add a bunch of variables by hand. The for-each step simply places the Sales Order on the internal Queue. The xform before the To Queue step, transforms the message into an individual Sales Order schema before passing it into the queue. Inbound is a txt file and outboudn is void.
Queue2SO
The Queue simply paces one Sales Order into the B1 Object atom. If there is an error, then a message is sent to a specified user in Business One. Inbound is the queue. Outbound is void.
Next I think I am going to try to see if creating an error queue will work as well.