LineageOS is usually referred to as Switchroot in here - and has nothing to do with your question, right? If if has - Switchroot doesnt support any 'Atmosphere' plugins like sys-clk.
The way sys-clk works in Atmosphere is, that it allows you to set clockspeed for GPU and CPU in a few different states (docked, handheld, charging, ...) on a per game basis.
The easiest way to configure it (once it is installed, and thats just copying over the correct files and rebooting) is - to also install and use:
https://github.com/SunTheCourier/sys-clk-Editor/releases
In there you can pick a 'donor' game / shortcut, set the overclock like you'd want to (usually only overclock GPU by one step max. CPU you can overclock a little more freely), and from then on, everytime you launch that game - it will get the overclock settings applied.
HBMenu works the same way. If you launch it though "holding R while launching that donor game you picked" it will launch HBmenu instead, with the overclock settings applied.
If you want a separate 'launcher' for HBmenu, that doesnt rely on launching a donor game (kind of a donor game itself), you can use:
https://gbatemp.net/threads/homebrew-menu-loader-legal-nsp.518433/
It works like any donor game (allthough with flycast, I had more frequent crashes using this than a real donor game - in all other cases it behaves just as any other game). But it is a .nro. Installing a non eShop .nro can get you banned by Nintendo, if you dont do it on an emunand, that never accesses the internet. So be aware of that. Installing this is optional, you can stick to using a donor game. (Thats just a disclaimer just in case you never installed a .nro before). Installing the .nro can be done with Goldleaf for example.
Why to use 'donor game' at all, and not just launch HBmenu from the Album shortcut?
Because only using a donor game (nro) while holding R allows HBmenu access to the full ram of the system, which you need for newer emulators (and some newer homebrew apps) like N64, PSP, Dreamcast and so on...
Donor game doesnt mean, that the game is gone, or will be modified, its just used to tell the system that you are launching a game, while you are launching HBmenu instead (thanks to holding R while launching it). The next time you launch it without holding R its back to normal (although still overclocked until you disable that through sys-clk(-editor)). Its an Atmosphere basic feature thing.
