When you go at attach the second sole, the slipper will be correct side out. You will be joining the inner sole ( which is the first one you knitted that has the slipper upper attached to it) and the outer sole together with a " 3 needle bindoff", even though if you're going to add the bumber you don't actually bind off yet.
As for as the inner sole being a different color from the outer sole, that's just personal preference (or maybe being a little short on the yardage needed for the sole). You can get really creative on the color combinations. I've done multicolor uppers by using two different color yarns for the upper, and a third color for the cuff. The outer and inner soles can be different colors, too. I've even knit a "racing stripe" down the center of the upper.
You could knit a rainbow clog if you wanted!!!
In the KnitAlong section of the forum there are two threads about the Fiber Trends Clogs with all knids of ideas!