Using dataFilter and htmlFilter for external plugins

Hello there,

I'm relative new to CKEditor and am trying to implement it into my application, however I find the API quite hard to follow.
Heres what I'm trying to do: in my app one can use plugins in their documents, for example for showing a list of other documents.
This is achchieved by placing a keyword (e.g. [plugin:563]) in the document source and replacing this by the pluginOutput on the frontend.
Now I'd like to port this behaviour into the backend (thus into CKEditor).
One would choose a plugin and see the pluginOutput as none-editable content in the editor; by double clicking it a dialog would open to let the user configure the specefic plugin.

I already made it half way by ripping the placeholder plugin apart.
The [plugin:563] placeholder gets replaced by the pluginOutput and is not editable but I can't achieve it the other way around for saving the document.

I don't see any way to get this to work..
Heres what should be done when saving the document:
Grab the previous inserted <div> container with the pluginOutput, remove it, replace it with [plugin:563] text.

Has anybody done this? I can identify the specific plugin-div in the htmlFilter but I have no idea at all how to replace it completely with text.

Thanks for your time,
Marco