This isn't a matter of settings but physical adjustment (the endstop switches). Having the head home slightly off the bed in the X and/or Y direction is a good thing, because it means the Z homing can't crash into the bed if the bed height is misadjusted. On my Ender 3, the X axis homes slightly into the bed, but the Y homes such that the nozzle tip is in front of the bed. Note that normally you don't try to print at X=0 or Y=0 anyway.
As for the Z homing, you have to adjust the bed height ("bed leveling") via the 4 wheels under the corners of the bed to bring it to the right height. If you can't get it below the nozzle with the wheels all the way tightened, your Z endstop switch must be installed incorrectly. The Ender 3's Z endstop bracket is supposed to fit against the corner of the aluminum extrusion just below it so that it doesn't need adjustment, but it's possible to mount it incorrectly higher. This is a bad idea because if it loosens it can move. It might also be possible to incorrectly install it lower, in which case it would be misaligned because the machine screws couldn't be tightened down all the way. This is also a bad idea. Make sure it's in the right place.
As for actual bed height adjustment/leveling, there are lots of good guides to that and I won't try to reproduce/improve on them here. The "sheet of paper" method is very good.