Here are a couple of hints which I have found useful with emdashes if (for any reason) the book cleaner files aren't working.
1. Edit your text in your word processor.
2. Use 'find and replace' to replace emdashes with # or@.
3. Drop the text into BD.
4. Use 'find and replace' to replace # or @ with a long dash.
This only takes a few minutes and I think that the result is worth doing.
I used to do it all the time until Jon perfected the book cleaner files.
After making the Sony Reader/Palm/Reb book, always remember to save the BD file. This means that you can go back and make corrections later. Either select 'Book Designer' on the make books tab (which is what I do) or move your 'last file' into the BD folder.