If "back to square one" refers to the cycling of the tank, then no, you aren't back to square one when you rescape the tank. When you prune stem plants and replant the cut off tops they continue to grow, using fertilizers just as they did before you pruned them. Stem plant roots seem primarily designed to hold the plant in position, not to feed the plant. In any case, the plants absorb nutrients from the leaves well enough to continue growing without roots. When I prune and move plants around I use whichever parts of the pruned stem plants look the most promising. Sometimes that is the bottom part if it looks like it has some good side shoots starting, but usually it is the top parts where the foliage is the best looking. A disadvantage of the bottom parts is that they almost always have lots of aerial roots, and I don't like to look at aerial roots.