Still like to know how to do this, specifically a two-handed war hammer and a bow.
You will find all upgrades under Enchantments in the list. Kurausu specified the possibilities for bows. For weapons (including two-handed war hammers) you have:
[Blacksmithing 2]
Boosted Metal Weapon =
Metal Weapon +
Whetstone (The Adventurer's Field Guide VIII)
(+ Damage)[Blacksmithing 2]
Boosted Metal Weapon =
Metal Weapon +
Whetstone Wheel (The Adventurer's Field Guide VIII)
(+ Damage)[Crafting 5]
Boosted Weapon =
Weapon +
Air Essence (Secrets of the Scroll VIII)
(+ Air Damage (max 1 extra damage type))[Crafting 5]
Boosted Weapon =
Weapon +
Earth Essence (Secrets of the Scroll VIII)
(+ Earth Damage (max 1 extra damage type))[Crafting 5]
Boosted Weapon =
Weapon +
Fire Essence (Secrets of the Scroll VIII)
(+ Fire Damage (max 1 extra damage type))[Crafting 5]
Boosted Weapon =
Weapon +
Water Essence (Secrets of the Scroll VIII)
(+ Water Damage (max 1 extra damage type))[Crafting 1]
Boosted Weapon =
Weapon +
Poison Flask (The Adventurer's Field Guide X)
(+ Poison Damage (max 1 extra damage type))[Crafting 4]
Boosted Weapon =
Weapon +
Tenebrium Bar (+ Tenebrium Damage (max 1 extra damage type))[Crafting 5]
Boosted Weapon =
Weapon +
Tormented Soul (Secrets of the Scroll VII)
(Strength: +1 (IL1) / +2 (IL14), Dexterity: : +1 (IL1) / +2 (IL14))I am not sure what you meant exactly by 'how', so I'll cover all possibilities
In your inventory drag the weapon over the component and release the mouse button, or drag the component over the weapon and release. A crafting dialog box should pop up if your crafting skill/blacksmith skill is high enough. If not a message will tell you it is too low. To use the Whetstone Wheel, just drag the weapon from the inventory over the Whetstone Wheel in the world and release the mouse button. The Whetstone Wheel will be highlighted with a yellow border.
I just verified that I could use a Tormented Soul to upgrade a two-handed warhammer. I also found out that the two formulas using whetstones does not work for two-handed warhammers. I will change 'Boosted Metal Weapon' to 'Boosted Edged Metal Weapon' in the next version since it works on swords and axes, but not on maces and warhammers.
As you can see these formulas are generic. That is because they generally work on every item matching the generic category, but there are exceptions. If you cannot upgrade a specific weapon, try another one. Maybe you have encountered one of the exceptions.
Lastly, you cannot upgrade a tenebrium weapon at all. If a weapon has tenebrium in its name, it cannot be upgraded.
Hope this helps.