I just got my bikes out of storage, and I've got to say, take a long, long, long trip soon after you get your bike. That way, you get bruises in your crotch. Take a few days off from riding and you're all set, no more saddle sores. I rode about 20 miles on back-to-back days right after I got my Trek out of storage. Ouch. But now, I hop on the bike and it takes a considerably longer time before I start getting uncomfortable.
If you are riding for fitness... don't be afraid to shift. Stay seated and try to keep the pace/heartrate steady. When you get to hills and such, downshift as needed to keep your butt in the saddle and keep the same pace. Sure, you won't be going uphill very quick, but it will keep your heartrate in "fat burn" mode versus "cardio" mode. Once you've lost your weight, then you can get more aggressive with the gears and work on speed/muscle/cardio.
And, as Budda mentioned, start on small trips and work up. When you add distance, decrease your rate the first time. Then, next time, increase your rate with the same distance. Then, add more distance/reduce rate, then increase rate again... etc. etc. You'll find it easier on the body to do it that way - you won't get your azz kicked as hard, and will be ready to ride the next day.
Oh, and don't be afraid to stretch before, and after, rides.