Yes, any bus going to Downtown Disney does make two stops there - one at the far end of the shopping area near Rainforest Cafe, and one near Planet Hollywood. When the water parks are open, these same buses do also go to Typhoon Lagoon - this bus destination should be pretty clear on both signage at the resorts and on the bus marquee.
In addition, Walt Disney World advises Guests to allow 1.5 hours to get to dining reservations when using WDW transportation. It's unfortunate that the OP's transportation took even longer than that yesterday, but if Magic Kingdom or Epcot were open when they were trying to get to the Polynesian, transferring at Downtown Disney would have been the LAST option anyone should have recommended!!!!