The advantage the keyboard has over the fret is that everything is in a nice straight line. With easy visuals like the black keys as you mentioned. 

But if you look at the fretboard in the same way and memorize where the "C" is on each string, you will begin visualizing the fretboard in the same way and with some time in you won't think twice about it and know what notes your fingers are on.

Not sure if that was your question but I interpreted your post as being concerned about learning the fretboard. Try this for a week and you will know the fretboard.