Assumption, use IBM Portal theme as template.
Themes:
Default.jsp
head.jspf
head_links.jspf
head_externalJS.jspf
Banner.jspf
banner_searchControl.jspf
banner_toolbar.jspf
topNav.jspf
sideNav.jspf
footer.jspf
Add customized CSS/JS for themes to a new folder.
Skins:
Control.jsp
UnlayeredContainer-H.jsp
UnlayeredContainer-V.jsp
Layout picture, referenced from IBM developer community:
