Ian,
You're definetly on the right track - yes, you can send in what is known as a Shipment as Work (SAW) to OTM. Difference is that SAW is an "after the fact" shipment. These transactions are rated and can be invoiced inside OTM frieght payment. You will need to send in an order release and also any relevant item or location information into OTM first.
Also, -RC integration command works great (we use it) but a word of caution as it can sometimes change the release/shipment configuration (ship unt level) AFTER you want to allow changes so proceed carefully. We saw several issues with release configurations changing after shipments were built and released to our warehouse to ship - not good
Let me know if you have any further questions and I'll see if I can help.
-Jeff