In Path of Exile, you may have those questions: What is the weapon physical damage? Is it the 31-78 dmg of the weapon? What is gonna happen when I would use Lightning Arrow? Only the 40% of the damage will be use for the random element? So I hope the following guide can really help most collectors of poe exalted orb.
Weapon physical damage is the physical damage from the weapon and added physical damage from your gear (Abyssus for example). If you use lightning arrow 40% of physical damage is converted to lightning damage. This happens after Doomfletch adds flat damage.
If you have 50-100 base flat physical damage, which includes gear, and 100% of physical damage converted to lightning, while using doomfletch's prism, you would deal a total of: 50-100 fire damage, 100-200 lightning damage, and 50-100 cold damage, with a default attack.
Basically, damage conversion is applied after everything else, so you never "lose" base damage just from converting it to a different element. It'll also still be affected by all relevant damage modifiers as it goes through the conversion process.
The way this conversion works is that all your phys dmg(((bow phys + flat phys) * sum of increased) * more1+moreN) is added as all elemental damages (in the case of doomfletch prism) and then gets converted to lightning in your case.
The way it works with doomfletch would be that it adds a random element and gets converted (but I'm not sure myself if and how the random part changes), but it should not be dependent on the skill you use.
If you are new to the game and don't want to mess up your first build, follow some build guide from https://www.u4gm.com/path-of-exile. Another option is to just mess around yourself and see how things work.