My OBJ exporter [and the Pro one as far as I know] simply exports the geometry and groups/instances-geometry in the order they are found in the SKP's entities context - this in turn is probably affected by the order in which they were placed into the model itself. There can be no control over the OBJ file's ordering.
As an OBJ file is basically a text file you could manually edit it with Notepad++ and reorder the hundreds of lines of code individual 'g' definition, but it'd be so easy to break it I wouldn't try.
Also we don't know how your third-party tool imports the parts anyway. If they are not in the order they are in the SKP but say alphabetical then as Dave says rename them !
You issue really isn't with Sketchup, perhaps it's with OBJ export, perhaps it about editing an OBJ file, perhaps it's about your other app - which you haven't given many clues about either 😒

Sounded like a nice workaround, but uploaded content can be downloaded as DAE only in paid accounts.

I also second Paint.NET - as a "starter". Very easy to use and if you erase a part of your image, it will automatically become transparent. There is a "magic wand tool" which lets you select colours like your white background. One click. Then press the Delete key and all is gone.

Under Window > Preferences > Applications, you can set your favourite image editor. Now if you right click on a face and go to Texture menu item, there is a possibility to edit the texture image. Do the deleting in Paint.NET and upon saving, it will automatically update the image in SU.

You really need something better than MS Paint.

transparent.png

@tig said:

There's an importer for Blender
http://www.blender.org/forum/viewtopic.php?t=18299&sid=7f24974c9439ea22c3f685a934fac0d2
So you could then perhaps export in an acceptable format ?

Oh, yes. I believe I've used that too, I just get erros the whole time.

It could be possible I installed the plugin in wrong, is there a guide for belnder plugins?

Also, would it be possible to write a Google Sketchup RB plugin using the data from that Python Plugin for Blender? It seems to have all the info you'd need if you can understand python, or even not, a lot of the code makes it obvious.