Live2D Free Version - Boxes around parts too big to move around texture atlas?

I've never used Live2D before, or anything even remotely like it. I'm following a tutorial to rig up my first model, and the current step is to arrange all the parts in my layers in the texture atlas. The tutorial tells me that I have to be sure that none of the parts or their meshes touch each other, and that I have to get the scale of all of them as close to 100% as possible. Since I'm using the free version of Live2D I can't make the size of the atlas bigger than 2048x2048 pixels, so I probably won't be able to get to 100%. But I could get close if it wasn't for an issue making it so I can't move most of them around.

In the tutorial video I'm watching, when she selects one of her parts to move it, the red dotted box that pops up around it is very close to the edges of it. But for some reason, those boxes around my parts are ridiculously big. This means I can't move most of them around the atlas; most times when I try to click on one to select it, it won't let me, instead selecting a whole bunch of parts with overlapping boxes.

I think the size of these boxes is the same as the whole canvas size of the drawing I'm using? Which is a problem that doesn't even have to exist because I just want to model the upper half instead of the whole body, but for some reason even though I've tried to edit the psd a few times in Gimp to cut off the bottom half, I'll put the newly edited version in Live2D and the whole thing will still be there. Either way it doesn't make sense for the boxes around every little part to be so big, especially since all the background is transparent. How do I fix this so I can actually move the parts around my texture atlas?