You would enter them on the K-1 worksheet according to entity type.  I haven't ever had to do this, so I'm not sure what the entity type is. 

You want to do your research and make sure your client is following the rules for his self-directed IRA's.  He cannot personally have any involvement in the running of the partnership that his IRA's are invested in.  There are very strict rules and I have found most people who have approached me with self-directed IRA's don't follow them.  That's why I haven't personally dealt with it.