Typically it is best to layout all framing , from the floor up to the roof, allowing space for chimney's, plumbing, ductwork, etc. Occasionally though, things just don't work the way we plan them. An engineered truss system should never be jobsite modified without contacting the truss manufacturer, to be sure that repairs can be made to restore the integrity of the truss. If modifications are allowed, the truss manufacturer will provide, in writing, how the repairs need to be made. A copy of this documentation should be submitted to the building dept., along with a complete set of truss specs.