When I use my digital recorder, I only say punctuation and use "new line". It looks ugly in DragonPad after transcribing, but when I copy and paste into Scrivener, I make sure to select "paste and match style", and it comes out just fine.
I did the recommended training on the recorder and have done little else other than to add words (character names, etc.) into the vocabulary file.
Transcribing commands never worked for me, so I dont even try and I get along just fine
In fact I would say (no pun intended) for me the commands are the weakest part of Dragon. I just spew out raw text and make it pretty in Scrivener. For me, it's way faster that way.