Mark all those places in the plan where seats and closets are to be. These places are given individually by ALCOVES (179), W'NDOW PLACES (180), THICK WALLS (197), SUNNY COUNTER (199), WAIST-HIGH SHELF (201), BUILT-IN SEATS (202), and so on. Lay out a wide swath on the plan to correspond to these positions. Make it two or three feet deep; recognize that it will be outside the main space of the room; your seats, niches, shelves, will feel attached to the main space of rooms but not inside them. Then, when you lay out columns and minor columns, place the columns in such a way that they surround and define these thick volumes of wall, as if they were rooms or alcoves.
For shelves and counters less than 2 feet deep, there is no need to go to these lengths. The thickening can be built simply by deepening columns and placing shelves between them.