Customising Modules - Eonic/ProteanCMS GitHub Wiki
Modules have all related files stored in a folder structure within ptn/modules/modulename and ptn/core/modules/modulename
If you are making changes to how a module is presented you have 2 options.
Create a copy of the entire module in your local modules folder /modules. Include the .scss and .xslt file in your local theme / installed modules.
rename the class to make it unique on both the scss and the xslt
pros - new features will be rolled out automatically other than the overridden module. cons - A little more overriding of the XSLT is required
exclude the ptn/modules/modules.scss file from you theme and create a local version excluding the css of the module you want to override, add the new css to the theme.
pros - no XSLT overriding cons - will not benefit from new modules css being added.
If you are only making minor changes you can do it in the theme but be aware there might be breaking changes to the common CSS at a later stage as the common CSS gets more polished. (Consider if your local change is a fix which would be better globally for all sites)
If you do want to make substantial changes to the ptn/modules consider creating a new version and deprecating the old. ???