What we're really discussing here is bike fit and set-up. Whilst there are several 'gold standard' positions for bike set up, the trick is adapting those to suit your anatomy, dimensions and riding requirements as required.
Regarding your specific problem, I'd suggest you look at your set up as a whole, taking into account handlebar height, saddle height, saddle position fore/aft, seat angle and possibly even cleat position as-well. I'd also check to see if you're riding a saddle that's wide enough for you (and no, that's not a posh way of saying you have a fat arse!)
Something to aim at: Don't sit on the squishy bits. These are not designed to be sat on. Imagine sitting on a table with your legs dangling over the table edge, you should be able to feet a couple of bony protrusions at the bottom of your pelvis taking your weight. When you set up your saddle, you should be aiming to make sure you sit on those bits, not the squishy bits! If your saddle is too narrow to allow you to sit on these, it's time to get a wider saddle. A couple of years ago specialized sent out what ammounted to a bit of memory foam on a board, the idea being that you sat on it, and could then see roughly how wide your arse was and you could then select an appropriate saddle, I'm not sure if these things are still around tho.
As a general rule with road bikes, I'd be inclined to start with the saddle completely level and then tilt it back slightly as a first adjustment. I know that this sounds counter-intuitive, and without seeing you on your bike there's only so much advice can be given, but the idea with this is that it rotates the pelvis back slighly, thus alleviating pressure on the squishy bits.
Hope the above is of some help.