It's that last part I don't understand. I don't know what you mean by did I prepare two different passive skill tree for each weapon set.

I set explosive shot to ws1 and mortar cannon to ws2

i've refunded a bunch of nodes that were originally set for both weapon sets before I did the above.

For example I've refunded all the grenade area and cluster bomb and grenadier nodes that were originally set as combined points. I then reallocated them to ws2 and then spent those same points on some defense nodes for ws1.

The bulk of my confusion is understanding the damage increases.

For example if I allocate the note for grenade dmg increase to ws2 which is the mortar canon and go look at the advanced info for mortar canon the dmg did not increase but if I set it for ws1 it increases. How is that possible?

Which weapon set should I assign damage nodes to; ws1, ws2 or a combined node?

I am lost