Hello Grimbot,
There are two different solutions to your problem.
First, you can of course create one big Photoshop file, which does not have to be messy at all, expecially since the PhotoshopToSpine script got updated today, and it has a bunch of amazing features that can be of help. (you have to re-download the launcher and you can find it into your Spine installation folder)
Second option, you can import the new assets on a separate skeleton in the same project, then you simply drag the attachments to your first skeleton and you need to reparent them to be done.
Please keep in mind that the json data that you export from photoshop to spine is not the same json data that you feed to spine, which you can obtain by exporting your project from spine instead.
To know more about how the script works here's the link: Images - Spine User Guide: Photoshop while for the new features just click help
in the script dialogue in Photoshop.

And here's more about export: Export - Spine User Guide