Comment 4 for bug 2000005

I have figured it out btw.
It's not very elegant but it's working.

So step one is to create a new theme in /usr/share/onboard/themes It will not work with the theme stored in the home-.local folder. Don't know why and don't care atm

What I did is that I copied the one I was using from /home/ME/.local/share/onboard/themes to the /usr folder. In my case "Blackboard".
Rename it (has to be done with "sudo cp") to BlackboardMod.theme or whatever you deem fit. Open the copied file with Nano and change the name accordingly.

Then you go into your /usr/share/glib-2.0/schemas folder and look for an override file created by LMDE called mint-artwork.gschema.override
In it you will find the lines

[org.onboard]
theme='/usr/share/mint-artwork/onboard/Nightshade.theme'
key-label-overrides=['RWIN:Super:', 'LWIN:Super:']
status-icon-provider='AppIndicator'

The "theme" line needs to be changed to /usr/share/onboard/themes/BlackboardMod.theme

Secondly the slick-greeter sets its own default value for the Layout in the glib schema "x.dm.slick-greeter.gschema.xml"
Nano it, find the lines saying:
    <key name="onscreen-keyboard-layout" type="s">
      <default>'/usr/share/onboard/layouts/Small.onboard'</default>
      <summary>Path of the onscreen keyboard layout</summary>
    </key>

And change "Small.onboard" to "Compact.onboard" (that is if you're using the Compact layout at all. If not ignore)

Rebuild the schemas with "sudo glib-compile-schemas /usr/share/glib-2.0/schemas"

Reboot. Done.

*note*
Ayn changes from running onboard will not be carried over to the /usr/ created .theme file. It will only apply to the /home/ configuration. So whenever you change the settings in your currently running onboard instance the changes need to be manually carried over to the /usr/ .theme file