By default the EQ is set to on and flat when you install iTunes in Windows too. Turning it off from flat doesn't seem to change anything but you might as well turn it off if you aren't going to use it.
The sound enhancer can do great things with small cheap pc speakers, but for any half decent rig, its usually better turned off.
Sound check is somewhat like replaygain, it compensates for differing volume levels between tracks by the use of attenuation. The problem with it is that it isn't so sophisticated that it is able to work between albums rather than individual tracks, and so (as an example) the Tracked Amarok, which breaks down a single 60 minute piece into its some 55 movements, loses its dynamic range (which is impressive and at times explosive) not completely but by a notable degree.
The soundcheck feature is useful however, for any time that you are say, having a party or another circumstance in which other people may be deciding on where the volume dial gets turned to. Its also useful for late night listening when you don't want a playlist to suddenly blast from Einaudi to Deep Purple.
As for turning these things off changing the soundstaging, this I am disinclined to believe. Theres nothing about them that should cause any channel blend.