From what I can tell by your screencaps it looks like it's the way the files are labeled in the Manga Publisher.
To make sure they all show up in the same row you need to have the "Manga" label in the Manga Publisher to be the same thing for all the chapters and volumes of whatever series you're working on. For example, volume 1 chapter 1 would have the same Manga label in the Manga Publisher as volume 2 chapter 1. eManga arranges the chapters and volumes based upon the values you input into the volume number and chapter numbers via Manga Publisher.
EXAMPLE

You can edit already added files by right-clicking and selecting "Get Info." Then just click over to the "Info" tab.
Hope that helps!
