Assume that you are using version 2.1.0. Create a folder custom under seafile-server-2.1.0/seahub/media. Put all the customization files here. The upgrade script will copy the folder to seafile-server-2.1.1/seahub/media when you upgrade to version 2.1.1.
seahub/media/custom/Overwrite LOGO_PATH in seahub_settings.py
LOGO_PATH = 'custom/mylogo.png'
Overwrite LOGO_URL in seahub_settings.py
LOGO_URL = 'http://your-seafile.com'
seahub/media/custom/, for example, custom.cssOverwrite BRANDING_CSS in seahub_settings.py
BRANDING_CSS = 'custom/custom.css'
Note: Since version 2.1.
Create a folder templates under <seafile-install-path>/seahub-data/custom
seahub/seahub/templates/footer.html to seahub-data/custom/templates.footer.html.seahub/seahub/templates/download.html to seahub-data/custom/templates.download.html.seahub/seahub/help/templates/help to seahub-data/custom/templates/help.help.