If the description of the mod says so.
For example, the "Unification Patch" has specific instructions. So does the "High Res Character Shadows and Lip Movement" mod. In those cases, you can't just copy the mod into your mod folder and be done with it (which is what the mod manager does, more or less), but they require you to copy different folders into different places, and so you gotta do it yourself. But in my case, the overwhelming marority of mods, 95% or so, can be installed with W3MM. It even has more functionality than Nexus Mod Manager. For example, when installing Friendly HUD mod (which requires you to install the Unification Patch, btw), the W3MM will automatically install all the key rebinds the mod has. If you manually install the mod, as far as I know, you gotta install those key rebinds manually by writing them into the input.settings file.
But don't think so much about it. Download it here:
https://www.nexusmods.com/witcher3/mods/2678
The description is long and quite imposing, don't let that scare you off. This program is such a quality of life improvement, it's absolutely a must have in my opinion.
Download it, follow the instructions to a T and manage your mods with it. Also, make sure to download Script Merger. It becomes a plugin for W3MM more or less, and it's very useful for detecting mod conflicts and resolving them.
https://www.nexusmods.com/witcher3/mods/484
I'm not sure whether you can install lighting mods with it. I mean I'm sure you can, but they might require manual installation so again, read the description.
Be mindful when installing mods. Always read the description and check out the comment section for eventual pinned comments by the mod author, or pinned conversations where something important was discovered or discussed. Also make sure to always check out the mod's files before you install it, and make sure to read the README file if there is one.
Sometimes modders put several versions into their mod's folder. For example the mod "Brutal Blood", you can't just install it, because inside the folder Brutal Blood there's not, like you would expect, the folder "modBrutalBlood", but two folders for two separate versions of the mod. So I recommend checking that with every mod before you install, because otherwise trouble shooting might be a nightmare.