The manufacturer creates a set of procedures covering the design process that meets, at a minimum, the stages set out in 21CFR, often following the industry standard for software: IEC-62304. Then mfr documents that those procedures were followed and at the end submits a set of documents about the test results and development process for agency approval.
Sound similar? One difference I can see is that if you replace the software in a released medical device with your own, it's no longer considered to be Approved and using it opens you up to Federal liability.