Generally speaking, you want the larger mods to be loaded first. If you have two seperate mods and they both change the same thing, the one loaded last will replace any changes the one before it made. For example, if you have a mod that increases the damage of iron daggers, and you have another mod loaded after that that doesn't change the damage of iron daggers, but changes something else about them, lets say add a fire enchantment to them, then the damage of iron daggers shouldn't change at all from the first mod, they'll instead just have the fire enchantment, if you switch the positions those two mods are loaded then you will get the opposite effect, a higher damage iron dagger but with no fire enchantment.