It's never too late!
Use the custom directory will save your life.
1) Under:
custom / modulebuilder / builds / MODULENAME / SugarModules / modules / MODULENAME / MODULENAME.php
here you can write your own custom class method.
add to repository the whole "custom / modulebuilder / builds / MODULENAME / SugarModules / modules / MODULENAME /"
2) Choose a whatever folder, in this case "zip" under:
custom / modulebuilder / builds / MODULENAME / zip /
you can put the source module builder package and add the "zip" folder to repository too.
Now each time you want to make a studio operation (for e.g. add/remove a field), once you made it, you can re-export the project and override
the archive file each time you want to commit.
Custom Icons
For the icons you need to modify and put on repository the following path "custom / modulebuilder / packages / MODULENAME / icons"
Production publish
The cool thing is that here if you go to "MB > PACKAGE > Publish" the generated module will have all your customization.