Proper way to use Include

I guess I need to put these JS and CSS into my Header include right?

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How you structure that, header and footer? I mean whats the criteria to be in header and footer? I guess if smth is globally or not. But what about Server Connections?
What I did now was, to :

1. Define one Masterlayout, Colours, Margins, Navigation, Header Logo, Footer Content, Sec. Provider
2. Define Header.php and Footer.php and put these values there
3. Check my list which pages needs to be created and Save these new files. Like, login.php, profile.php, logout.php, index.php etc etc.