I have had very little experience with any Citrus so I'll have to pass on that one. Pomegranate will back bud on old wood so what this means is that there is no hurry to do any pruning. Let them grow freely for a year or two then cut them back. After the first cut you'll get several branches down low. This begins the process of introducing movement and taper.
Allow these branches to grow in order to thicken the trunk. No need to prune these either except to avoid reverse taper. I don't usually allow more than one branch at a given level, any more will eventually create a bulge. If you allow more than one at first keep a close eye on that location and prune all but one out before a bulge begins.
Roots; it's never too early to begin to guide the roots into a pleasing arrangement. This means keeping roots all on one level and in a generally radial pattern. This is an ongoing process started at the first re-potting. Don't prune the roots any more than necessary in fact try to keep pruning of any sort to a minimum, it will only slow development.
Developing a bonsai is an entirely different game than maintaining an established tree, this is one of the things that many books tend to gloss over. For instance, often you'll read to prune new shoots back to one or two sets of leaves. Treating young material this way is counterproductive. Growth of the trunk, branches and roots is necessary to create a bonsai of merit in a reasonable time frame.