Yup. You got it. The only place I have found in BeerSmith for dead space is for the MT. If there is a place to calculate HLT, BK, etc. I have yet to find it.
However, in the water tab, be sure to calculate your post-boil loss to evap, deadspace, trub, hoses, etc. This greatly effects your pre-boil volume as well as what you plan on putting in the fermenter.