Ottawan,
I wouldn't necessarily remove the shoots below the soil. If you have a good strong soot, it will grow out of the mix fine and I wouldn't want to get rid of it. If it is small, then maybe. Nothing hard and fast about cutting these away. I just suggested that if you have more than 2 shoots, you might want to remove the "extras". I do. This way all the growth energy is focused on the 1 or 2 you leave behind and on root development. This is based on what I have observed with my cuttings.
For example: on an Atreano cutting, there were 3 thin branches developing and a few new leaf buds starting to develop. All were equally gaining length but not thickness or leaf size. I cut away everything but one main shoot and now it is gaining length, thickness and the leaves are increasing in size. To me, I'd rather have 1 healthy main branch then a bunch of weaker ones. I've seen this and done the same with several and it seems to help them mature faster.
As far as cutting away shoots below the soil, I've done both - leaving them and cutting them off. I would base that decision on how many shoots there are, how strong they look, and how thick the roots are when you transplant it to rooting media. The goal being to thin it to the best shoots to conserve energy at this stage and get them to the point where they are generating energy via photosynthesis (this takes a little while to establish). Then it becomes only a matter of preference on what form you want the plant to grow in.