For learning the basics on how to use the tool, see this post and also this post
It is now possible to import scaled up textures, meaning you can for instance edit a 512x512 texture, scale it up to 1024x1024 in the image editor, save, and then import with "Save changes" in the JSRF ModTool Texture Viewer tab, the tool will import the texture with the new resolution.
This will be useful for some of you out there who want to re-create some of the UI textures which are quite pixelated and low resolution and could use an HD remake, looking forward to those mods.
The tool maximum texture resolution import is limited to 2048x2048, I haven't tested higher resolutions and really for JSRF I would recommend sticking to 1024 as the maximum in general.
And as always, don't forget to clear (delete the files) in the cache, that is the X Y Z, HDD partitions, so the game reloads your modded files.