Exporting Questions

The secret to rigging is having the right layers and hierarchy. That way, most of the rigging is handled automatically and you just have to manually rig the appendages. Fortunately, @oksamurai has made a blank template with the layers already named and sorted for you, here: https://okaysamurai.com/puppets/TemplateBlank.zip Eventually, you'll become confident enough to set up the layers yourself. 

I suspect you will get faster at rigging the more you do it. Getting the layer names right by default so things auto-rig as much as possible helps. (There are little tricks like special names bind keys to triggers and things somewhere - I never use it myself.) 

What I don't recommend: use the same root name for every character - then export the puppet (via menus to create a .puppet file), import it again (this will make a copy of rigging AND artwork file), then Edit Original to update the artwork. As long as no names are changed, rigging will not be lost. I don't recommend it as I like unique root names for puppets, but as soon as you rename the root it thinks you deleted the old puppet contents and created a new set of rigging. But it will work... until you start changing the artwork file hierarchy.

(Note to self: I wonder if Adobe could add a "rename and preserve rigging" option... but it would have to edit the original artwork file, so probably too hard. Or maybe if CH ignored the root name, if only one root, it would allow an artwork file to be renamed without losing rigging. That would reduce re-rigging effort... I don't think you can copy and paste rigging between puppets.)

One thing you said I did not quite understand. "...so that when i import them all into 1 scene they don't share the rigging links". If you use "export" and "import" from the menus, each imported character is an independent copy. If you "duplicate" a puppet inside CH, a copy of the rigging is made by the artwork file is shared (the "Path" property is the same). You can certainly have multiple instances of different (or the same!) puppet in a scene and animate them separately. I might be missing your point here.