Katie, in order to visit the Great Sand Dunes, you'll take 160 to Monte Vista. From there, you can take several small county roads to the Great Sand Dunes, but probably the easiest (fewest jogs/turns) is to head on east through Alamosa and take County Rd 150 north to the Sand Dunes entrance. When you depart, you can take the county road that goes west past San Luis State Park to intersect CO 17. Turn right and head north to intersect 285 north to Poncha Springs and Nathrop. From there, to get to the Florissant Fossil Beds, you take 24/285 east. That turn off is a few miles south of Buena Vista. Continue east on 24 to Hartsel and Florissant, where you turn south to the Fossil Beds.
Where you stay the night will depend on how early a start you get when you depart Pagosa Springs and how much time you spend at the Sand Dunes. You could drive to Colorado Springs from Pagosa Springs in a day with a quick stop at the Sand Dunes and the Fossil Beds, or you could break it up with an overnight or two along the way. I'd probably stay one night along the way so you could stay two nights in Colorado Springs before you set out for home.
You could stay in Alamosa or the lodge near the Sand Dunes entrance, or you could stay in Salida or Buena Vista. You could also stay at the Mt. Princeton Hot Springs, which is west from Nathrop. (Great hike to Agnes Vaille Falls nearby, too, and St. Elmo ghost town a few miles further west) My choice would be Mt. Princeton Hot Springs or Buena Vista.
Another fun stop is the gator farm (lots of other animals, too, as the farm rescues and cares for other exotic animals... and a great place for bird watching, too).