Originally Posted by jayhuse
I am new to biking...
This may be the answer to your question.
Soft saddles will be uncomfortable after ~10 miles. A saddle that is too firm with little padding will also be uncomfortable.
Your sit bones and butt aren't used to sitting on a slender seat and you have to give that part of your anatomy time to get used to the saddle. After a few weeks you should be used to it and you may find that the saddle is very comfortable.
Another problem you may be experiencing is riding a road bike for commuting. Twenty miles each way is a lot of time in the saddle if the roads you're riding on are typical of most city roads -- potholes, broken pavement, trash in the road, etc. Road bike frames aren't always built to absorb or dampen the constant shock and vibration caused by crappy roads. Road bikes are intended to be ridden on fairly smooth roads.
Perhaps you should save the road bike for weekend rides and get a bike that is better suited to commuting. My personal choice is a cyclocross bike. Other folks ride hybrids or mountain bikes.
Originally Posted by jayhuse
I already have a pair of good biking pants with the padding in them along with good biking underwear.
Oh no! Here comes the UnderWear Nazi.

By "pants" I'm guessing you mean shorts.
Underwear isn't necessary when wearing
padded bike shorts or tights. Commando is the correct way to wear them!!
I'll let the UN fill you in on the details.