Another area of issue in the past:
1) Tools that could be duel use:
In this case tools such as those used in farming, logging, ship building, smithing, etc that can also be used in combat were generally seen as using the general spell vs the weapon spell.
a) areas where it is different: weapons such as a war hammer that also had smithing powers, ie it is a war hammer first and a tool second.
b) a lot of farming tools can be used as weapons, such as flail's, sickle's in eastern martial arts as weapons were often restricted.
c) Your Game: IIRC the weapon enchantment was more expensive then the general enchantment so you could say all duel use items have to use the more expensive enchantment.
game effect: if you let players use the cheaper method all the time it may unbalance your game in the long run...but... using the more expensive method for all duel use items means a lot of common use tools are going to be potentially a lot more expensive and thus rare in the game. ie no +10 magic plow +20 to cutting roots.
2) You Could:
You could define where the bonuses go so they do not go other places, ie a +10 general spell says in the text (because you have defined it that way) to only apply to "crafting" checks. But then you might also need to have enchanting spells and or effects to make your object more durable and resist other effects by using another spell thus making the craft item more expensive then a weapon.
Example: You create a smithing hammer, +15 to all smithing rolls, then it needs an heat and cold resisting spell, durability/strength/reliability boosting/resisting and or repairing spell or maybe even a new general enchantment for each type of smithing you want to bonus to apply to (weapon/armor/black smtihing/jewelry/ gem creation (from Middle Earth and or RM2 EC)/etc).
MDC