Manual mode refers to the settings on your camera that allows you to manually control aperture, shutter speed and ISO. Together, these three elements combine to effect the exposure of your photographs (how light or dark they may be), which in turn impacts the general appearance—and sometimes quality—of your photos.
The difference between shooting your photographs in automatic vs. manual means that when you shoot in automatic mode, you are letting your camera have control over these aforementioned settings as opposed to you having direct control over them.
Many people are very intimidated by shooting in manual mode, especially those who are relatively inexperienced or new to the art of photography. So while you can choose to let your camera do the heavy lifting for you, choosing to operate in manual mode gives you way more creative control than the former.
For example, if you choose to shoot in manual mode, you have direct and explicit control of just how your photos turn out. When you have complete control over shutter speed and aperture, you get to decide how your completed work of art will turn out. If you let your camera determine these things for you, you lose a lot of your creative control and opportunities to truly make the shot your own.
If you surrender control to automatic mode, you cannot physically and personally control your aperture, which means you don’t get to choose how focused or unfocused your shot will be.
Moreover, you cannot control the shutter speed if you choose to work in an automatic mode. Maybe you want more blur or less blur—if you want to dictate that choice, shoot in manual mode!
Additionally, manual mode lets you take the reigns on how bright your shot will turn out. This is made possible by manually determining the shutter speed, aperture and ISO, which you cannot personally determine in automatic mode.
So the choice is pretty clear: if you want to make sure your shots come out exactly the way you personally desire, you should consider ditching the automatic in favor of the manual.
Be aware that mastering the manual settings takes time, so practice is a necessary activity. At the end of the day, shoot in the setting that makes you happiest because that will really show through in your end product.