1. Make sure your bicycle fits first. One of the leading causes of saddle discomfort is an incorrectly set up bicycle.
See this link for bicycle fit advice:
http://www.cyclemetrics.com/Pages/Fi..._fit_links.htm
2. Get a good saddle. Make sure it is wide enough for you, but not too wide. It needs to be wide enough so that you sit on your sitbones, but not too wide to cause friction issues and misalignment issues. You may also need to determine whether you like a flat saddle or a saddle that curves up in the back. I need one that curves up in the back or I get lower back pain. But others like a flat saddle.
If your bicycle fits and you've got a good saddle, you shouldn't need padded bicycle shorts ... especially not for short rides.
With a properly set up bicycle and a broken-in Brooks saddle, I've been able to cycle up to 80 km in a bathing suit and beach shorts.
If you do want to go for padded shorts, remember that you don't need to spend a lot to get comfortable shorts. My favourites are the least expensive MEC ones. Don't be afraid to try inexpensive shorts. And also remember that quite often less is more when it comes to the padding. The padding should cover your sitbones ... you should not end up sitting on the seams ... but as for the thickness, many riders (myself included) find that thick padding, and especially think padding with all those sections and lumps and bumps that some cycling shorts padding seems to have, causes more problems than it solves. My second favourite shorts are very inexpensive Nashbar shorts with next to no padding.
The key is to try several pairs of shorts on in the store ... sit in them, squat in them, move your legs up and down in a pedalling motion, straddle something in them. Make sure they've got the flexibility you want and that you feel comfortable in the material. Reach around behind you and check to make sure the padding covers your sitbones. Take your time making your decision. Pick a bad (for you) pair of shorts and you will regret it.