If your saddle is comfortable for short rides but not so for longer ones, it's too squishy and not supporting your sit-bones. Find a chair that you can sit on, such as a dining room chair, and lean foward, aiming to touch the ground. Then get up (and provided it's a squishy cushion) you should have a bum imprint, with 2 deeper visible imprints relatively close together. You will notice thats where the most pressure on your butt was when you leant forward-measure these dimples. Now you need to find a harder saddle to suit-with a width slightly wider then what you measured your sit-bones at. A great tip is to use this website for reviews on different saddle's your research mentions. You are most importantly looking for saddles used by people in similar sizes and weights to you, not featherweights at 120 pounds like I. This is how I found my saddle-Selle Italia SLR XP, which heavier riders found shocking, but lighter riders at roughly my size and weight found wonderful.
Also, if that same LBS fitted you in the first place, then It's time to tinker or try somewhere else. If you have one, set your bike up in the trainer, with new saddle fitted, and find out where your weight is dispersed on the bike-are you using your hands excessively to hold yourself up? This will normally be accompanied by numb hands. Are you reaching so far foward that weight is distributed over sensitive area's? Could be time for a shorter stem. Maybe your knee's don't feel "quite right" or to get your weight evenly distributed, you have your seat adjusted foward a lot-time for a seatpost with less setback. The saddle should either be very very slightly toed down, or preferably parallel as a reference point for further adjustment-I use a builders level.
The key to comfort is equally distributing your weight over the pedals, saddle and handlebars. Don't worry about aerodynamics-get comfy and enjoy yourself. And don't be afraid to tinker a bit-if you're worried about making it worse, mark things with whiteboard marker or permanent marker. If you do screw it up, you could always go back to what you had.
Also, try the new position out for a while-say 100 or so miles. That gives your sit bones time to give you some feedback on the new saddle, e.t.c. I know my butt was sore the first 2 rides I used my new saddle, but since then, spot on.

Hope I've helped and best of luck!