Puzzling out weapon set passive skill points in Path of Exile 2 is perhaps the most cryptic part of the game I've encountered so far, mainly because the UI doesn't explain it properly. These skill points are a special allotment you can attach to your first or second weapon set, effectively giving you two separate skill trees that are only active when you're using each weapon.
If you're sticking to your class quite rigidly in terms of weapons, this might not be for you, but if you want a ranged weapon and a melee weapon, say, you might consider using these points to create a slightly different passive skill tree for either. This mechanic really comes into its own in the endgame, when you'll have a lot more points to work with as well as more weapon set skill points. But for now, there's no harm in finding out how it works.
So let's start at the beginning. In Path of Exile 2, you can have two different weapons equipped at once using the I and II tabs in your character loadout. If you navigate to the passive skill tree, you'll see two options in the top right saying 'I weapon set' and 'II weapon set' with a number listed in brackets next to it. This is how many weapon set skill points you have.
If you've just started playing, you won't have any, but as you defeat bosses you'll earn the occasional Book of Specialisation, which you can consume to get two. You can also get some through certain skills as part of your Ascendancy—when you choose an advanced class to upgrade to.
Now, the most important thing to note about weapon set skill points is that they don't actually count as additional points. Think of them more like a capacity, i.e if you have six weapon set skill points that means you can allot six points into weapon set one or weapon set two. That number represents six points worth of customisation when you swap weapons.
Still with me? If neither of the two weapon set tabs are clicked, you'll allot skill points into both when you level. So, let's try allotting one to a single set in practice (once you have at least one weapon set skill point):
This illustrates the nodes you have active in either set as you switch weapons. You'll also see the number next to 'I weapon set' has changed, since this indicates how many weapon set skill points you're currently using in each set.
If you're really planning to use these points and spec into multiple weapons, then you'll want to think carefully about how you arrange your passive skill tree. You should select nodes that open access to lots of different skill options, since this maximizes what you can use the weapon set skill points for.
You might also consider dipping into the other class' passive skill trees on either side, especially if they're a class that specialises in the second weapon you want to use.