Here is some general advice:
https://www.dokuwiki.org/install:upgrade
The one thing it seems to be a bit vague on is handling the template, especially if you are using one of the pre-installed templates. Here the best advice is to put your user-defined template styles in conf/userstyle.css. If it doesn't exist, create it.
See:
https://www.dokuwiki.org/devel:css?s[]=userstyle.css
If you are starting with Dokuwiki now, using the upgrade plugin makes upgrading a snap:
https://www.dokuwiki.org/plugin:upgrade. You should still put user-defined css in userstyle.css.
If you need custom javascript, you can include it in conf/userscript.js or in script.js in your template directory. See:
https://www.dokuwiki.org/devel:javascript.