Don't think the bus interchange would be inside the Watertown mall. The bus interchange could be shifted next to Watertown, since the marketing materials mentions that "The Punggol MRT and LRT Station, and Bus Interchange, is seamlessly connected to Watertown" (from Far East's marketing materials).
From what I have read about Watertown mall, the mall would be made up of retail outlets, with cinemas in basement 2. The car park lots are also in the basement levels, if I recall correctly.