Work on your own theme, not a built-in one. Create a new theme or extend an existing one first — LimeSurvey updates can overwrite changes made directly to a built-in theme. See Creating a New Theme.
Just adding your own CSS or JavaScript? You usually do not need to touch config.xml at all — put your rules in the theme's custom.css and your code in custom.js. These are loaded for you.
Registering additional CSS or JavaScript files is what config.xml is for:
/css or /scripts folderconfig.xml, add the file paths to the <css> or <js> blocksExample configuration:
<css>
<filename>css/jquery-ui-custom.css</filename>
<filename>css/bootstrap-slider.css</filename>
<filename>css/awesome-bootstrap-checkbox/awesome-bootstrap-checkbox.css</filename>
<filename>css/flat_and_modern.css</filename>
<filename>css/template.css</filename>
<filename>css/myCustomPlugin.css</filename>
</css>
<js>
<filename>scripts/template.js</filename>
<filename>scripts/bootstrap-slider.js</filename>
<filename>scripts/myCustomPlugin.js</filename>
</js>
Not seeing your changes? Clear the LimeSurvey cache after uploading files or editing config.xml — cached assets are the usual reason a correct change appears to do nothing.