You didn't say what the mature height of each tree is expected to be, based on its rootstock, but that is the main determinant of how many tiers of scaffolding will fit on the tree. If the first cherry is supposed to end up as a 12' semi-dwarf and you start the lowest tier 3' to 4' off the ground and space the tiers 2 to 3 feet apart, the third set of scaffolding will likely be the last up the tree and then you will keep the leader in check. That's the overview. Your objective now is to get these very young trees pruned and trained to a good start. On tree #1 I'd start over by removing the two branches that appear to be near the bottom of the tree (it's hard to tell from the photo) and stub cut what's left at about 3'. On tree #2 I'd leave the leader alone for now and see if you get some shoot development where you cut off the "competing lateral" that might provide nascent scaffolding. I'd also try training those lower branches to a lower angle. On tree #3 I wouldn't trim the scaffolds but thin out shoots too close to one another. You want to have scaffolds that if you were looking down on the tree from above would appear to be at the 12 o'clock, 4 o'clock and 8 o'clock positions. From the photo those scaffolds on the left side of the tree look as though they will be competing for the same rays of sunshine. I think one's got to go.

Eventually you'll probably want to convert the cherry to open center anyway as they crack less the more open the tree is so you might as well butcher the sucker where you want your scaffolds. Leave the lower branches just in case.

Choose your new scaffolds early in the growing season (they will appear near the cut) and pinch them back maybe 3 times. Keep selecting one shoot as the central leader of each scaffold and subdue the rest to be your secondary branches. Ultimately the secondary branches should be less than half the diameter of the central leader of your scaffold at point of attachment to the scaffold.

I have found it entirely safe to prune young cherries extremely aggressively when they haven't been trained right.

The nectarine looks fine. Maintain it as a central leader for a couple of years and don't let the top dominate the branches you want as your permanent scaffolds (summer pruning will help). You'll want to cut out the top and convert this tree to open center as well, once it is established.

Thank you for taking time to reply! Here are some secondary questions if you guys have the time.

So to overview, it sounds like you guys both agree I should basically whip (I think would be an accurate term) the first cherry again? I think I would leave at least 1 of the lower branches and see how it does.

@harvestman: When you say choose the new scaffolds and pinch them back...can you clarify for me please? I'm not sure exactly what you mean, and I've been doing so much reading regarding all of this lately it is all starting to blur together!

For Cherry #2, it sounds like it just needs a bit of training and some wait-and-see? So it is okay not to let it go a couple of years before opening the center as long as scaffolds are developing? Do you normally want to bring the top down some each dormancy to keep it from getting too tall?

For the nectarine: Also seems to be in relatively good shape, and just needs some thinning and trimming of the smaller shoots that aren't growing in a desirable orientation.

Also, summer prune the central leader to make sure it isn't shading the laterals too much.

Am I processing all of this correctly? So much to learn!

Thanks again for the hand holding! I obviously just learned this last year the importance and need for pruning as I dove head first into fruit trees :)

When you cut the cherry to the height you want first scaffolds, several shoots will grow right at the point of the cut. If you wait until growth begins to do this you are more likely to stimulate buds to grow further below the cut but at any rate, cherries tend not to do a good job of making secondary branches off of their scaffolds.

When shoots start to grow you can save the most vigorous upright one to be the temporary central leader. Then select the growing buds that are positioned well to be your scaffolds. After they've grown out about nine inches pinch the tip. Hopefully several shoots will sprout out where you pinch. Once they are a few inches long pinch the very tip of all but the straightest one to slow them down and let the straight one dominate. You can repeat this process a couple time during the growing season.