Saddle Up(s and downs)

For this first time in my time as a triathlete... I'm dealing with the most dreaded issue of all.  Oh, I've heard others talk about this (in great detail too, which I'm going to try to spare you from).  I got a new bike saddle.  I rode it on some hilly courses where I wasn't exactly aero the whole time.  I thought it was totally fine, but being in aero on it for 3 hours of nonstop aero started to hurt around mile 30.  It was too much pressure in all the wrong spots and I'm now totally bruised up because I buckled down and pushed through the pain for another 26 miles.  I took a week off to just swim, jumped back on the saddle on Saturday for some fun out on the East end of town and now, 50 more miles later, and an uncomfortable run yesterday, I'm having to take time off training as swimming and running are aggravating it too.  I'm not happy.  I hear I might not be sitting on the saddle correctly.  There's no real answer... its all trial and error.  Look, this is part of my IMWI experience and could be just a blip I'll laugh at later or could really derail my training for a little while.  I'm currently trying to avoid the whole freak out and panic habit I often have... but  I am worried about the 100 mile hilly Gran Fondo I have planned for this weekend.  I can take my road bike, but are my ligaments/tendons/hip flexor muscles going to be recovered in time?  Did running on it yesterday make it worse?  Oh, goodness.  Still, ever since I've been blogging... I still have not learned to handle soft tissue pain with any sort of ease!  At all.  I am pretty sure its at the very least some massive internal bruising.  OK, I'll stop there.