Every hard drive has bad sectors when they are produced. When the manufacturer initially sets up the drive, they record them in a special list, call the PLIST. This list is, to the most part, static. More bad sectors can be added to the list, but that requires special tools to make it happen. Then, there is the GLIST which houses the bad sectors that come along over the years of use. This list is managed by the hard drive itself. With the aforementioned tools, the GLIST can either be cleared out or transferred to the PLIST. To add to these lists, the operating systems (ie, Windows) keeps tracks of what it considers bad sectors and marks them as unusable.
So, yes, there really isn't much to worry about 2 or 3 bad sectors. However, the drive needs to be closely monitored because 2 or 3 bad sectors can very quickly turn into 2 to 3 million bad sectors...it really depends on the causes for the bad sectors being formed. If they are there because of minor media defects, that is one thing. If they are there as an early sign of failing read/write heads, then you want to watch out.
Now, to the software tools. I agree that the manufacturer's software tools are always best for each drive. Be sure to run the most thorough scan that tests each sector with a read and a write. This is usually done through a low level format. In doing such tests, be sure to backup your data, as the drive will be super clean when you are done. If done correctly, the data cannot be recovered, not even by a
hard drive data recovery service.
Other tools that I have used are Drive Fitness Test by Hitachi which works with all brands of drives and is free and Quick Tech Pro by Ultra-X which is a commercial product that tests all your system hardware, as well.
Good luck with your drive.
Luke