I imported 6 tables into the deployment toolkit and the existing indexes and relationships do not appear within the database profile.  I understand triggers are not support, however shouldn't the indexes and relationships come over?  Also, what about constraints?

I understand   I do not know the exact timeframe that this enhancement will be added.  I will say that we have a collection of enhancements that we are planning to make to the DDT that would be very helpful, which includes this request.  It was our inital goal to have this in the 1.5 release, but I cannot say for sure if this will be in that update.  But this feature will be added soon as it has been requested a number of times.