Hi,
Its basically implement a control that wraps the editor then implement an adapter to configure it. Compile it into your own dll, put it in the bin and add an entry to mojoEditor.config or ideally copy that file rename it and then reference your custom file from user.config by override the setting:
<add key="mojoEditorConfigFileName" value="mojoEditor.config" />
that way you won't lose your custom settings on upgrades.
Note however that I'm currently working on improvements to our TinyMCE integration and I plan to make it the default for new installations as it will be our best one after the improvements.
I've already implemented our Content Templates and Content Styles and now I'm finishing up a new file browser for browsing/uploading images and other files. Its going to be very nice.
Best,
Joe