You can provide all necessary additional files (mxds) in a zip archive. To further protect them you can set password for such archive or compare checksum.
In order to do it you need to write and use python script in your module. Just create script which will unzip your mxds to some temporary folder. Then add this script to your Toolbox and use it in you model in Model Builder.
Another way is to export your whole model to python and perform further development there. I am usually prefer this way in cases when I am facing additional more complex processing tasks and have needs in other libs.
Here is some points to start from: