I didn't read the other replies, but sounds like you might need a different saddle. Maybe something with a cut out, though not necessarily. I used to have a similar issue as you (though not as severe). I had the Terry Damselfly. I now have the Selle San Marco Mantra. It has a very big cut out and my "parts" don't get squished.

Everyone is different as to what works for them, so you probably need to try several saddles to know what will work for you. There are some stores that will let you ride around briefly on a saddle to at least get an idea if it might work. Performance Bike (.com) has an unconditional money back guarantee, so you can buy it, try it and return it at any time for a full refund or exchange. I just found out an LBS in my area will let you buy a saddle and you can "exchange" it and keep trying new ones until you find the right one. No refunds, buy they'll let you keep trying new ones.