You can wait until 1.7.0 (release is on Monday), the base template has been decomposed into separate header/footer/metadata templates 🙂
Documentation-wise, it's being re-written at the moment, developer guides section is under internal review atm: https://ignatberesnev.github.io/static/dokka/docs/1.7.0-SNAPSHOT/developer_guide/introduction/
User guides is next, I'll write a proper tutorial for setting headers/footers and templates as well as other settings.