I was where you are now early last October. I'm a 45 year-old smoker, never been overweight, but hadn't done any serious exercise in years. Decided to try and get in some kind of shape, did some research and bought a good road bike. When I first got it, I could barely get it around the block and I didn't like it at all - I HATED that thing. Problem was that it cost so much, I couldn't just let it sit there. So, I forced myself to get on it almost every night. Saddle soreness (reminiscent of my first ten speed in high school) went away pretty fast and I was doing five miles a night in no time. Ten miles a night came pretty fast and I held it there for a while; then started to add a bit. By late December, when the weather got real nasty and I had to park it, I was up to 15 - 20 miles a night and a 35 mile ride on the weekend. Got back on it in early March and was back where I left off almost immediately, albeit a bit sore during the first week or so. Did my first 50 miler in April, did over 60 miles today for the first time. The progress continues to amaze me and, needless to say, I LIKE the thing now - and it just keeps getting better.
So, from my limited but fresh experience, I would advise you to just force yourself to ride the thing regularly; try 30 or 45 minutes. Your speed and endurance will increase before you know it. It's okay if your legs get a little sore, that seems to be the price of admission, but it will get much better as your muscles develop - and that seems to happen pretty fast.
As far as gears are concerned, if you have three gears on the peddle crank, leave the chain on the middle one. If you have two gears, leave it on the small one. Practice with changing the gears on the rear sprocket only and you'll get the hang of it pretty fast. Once you are comfortable with that, experiment with the front sprocket too and you'll get the idea. You will note that you can achieve the same "speed" by using different combinations of the front and rear sprockets. Once you're using both sprockets, try to keep the chain as straight as possible, e.g., try not to ride with the chain on the big front sprocket and the big rear sprocket at the same time (or small/small). It's okay if that happens a bit while your learning, but it's bad for the chain over time as it causes it to run at an angle.
The purpose of the gearing is to allow you to ride at a constant cadence, you shift up or down to maintain the same RPM on the crank. I didn't even think about this until I had ridden the bike enough to be able to maintain a constant cadence - so I wouldn't be too concerned about it at first. When I finally checked it, I found that my natural cadence is 75 RPM. That's on the low side of "okay," but I cruise along at 20+ mph on level roads and climb grades easily that seemed like insurmountable barriers just a few months ago. Once you get used to the bike, you may find this to be a non-issue for you as well.