Normally the EV for your scene is measured by the camera's metering system and you use exposure compensation to set +EV or -EV when you know that you want to adjust the meter's result to guide the camera in it's exposure decision.
If you shoot on manual, you are controlling the entire exposure (aperture, shutter speed and ISO), so you are in effect "setting the EV" although I've never seen it written like that.
... According to the manual,when taking a photo with lots of sky, it recommends setting to +3 EC or +1EV
That's probably because the EC (exposure compensation) on your Fuji is set to increase or decrease the exposure by a third of a stop.
So if you dial in +3 EC you're actually increasing the exposure by one whole stop. Conversely, if you dial in -3 EC you're decreasing the exposure by one whole stop.
....does that mean that rather than messing with EC I could just put the camera in auto and note the aperture and shutter settings say for example F5.6 at 1/125s then go into manual and set my shutter to 1/125s and increase my aperture to F8?
Thank you for your reply, Having read your post does that mean that rather than messing with EC I could just put the camera in auto and note the aperture and shutter settings say for example F5.6 at 1/125s then go into manual and set my shutter to 1/125s and increase my aperture to F8?