You dont need to mark bad sectors manually. Hard disks have a pool of spare, good sectors. When bad sectors are found they are automatically flagged and replaced by spare, good ones. All this is invisible to the user.
FYI, you can use tools like Crystaldiskinfo and HD tune to monitor bad sectors, if the drive is SMART enabled (most drives are). However, please also run a hdd diagnostic (depending on your hdd brand).
Harddrive diagnostic Tools and services - Tacktech.com
A few bad sectors are normal after a period of use. You should backup critical data from that disk on a priority basis. Unless the bad sector count is extremely high, keep a watch over it, particularly for sudden increases. When that happens, be prepared to order a new drive.