Still have no idea what you meant by your explanation. I'll give you an example of what's confusing. It's from the OSX dictionary widget.
1) "My father's warnings had no effect on my adventurousness."
2) "What you eat can affect your mood."
To me, the usage of the two words is the same, or very similar. The sentences have a similar structure. The first part of the sentence (ie: "My father's warnings" and "What you eat") has some impact on whatever is mentioned in the 2nd part of the sentence (ie: "on my adventurousness" and "your mood").
You couldn't be more wrong. I'm willing to bet that most people here don't know how to diagram a sentence, let alone know what each part is, but since it's still fresh in my high school mind, and I'm procrastinating real homework, I went ahead and diagrammed the two sentences for you.
So, in the first sentence, 'warnings' is the subject. It is modified by 'my' and 'father's'. (Yes, it would make sense that 'my' would modify 'father's', since it's not my warnings, but 'my' and 'father's' are adjectives, and adjectives can't modify other adjectives.) 'Had' is the verb. Pretty simple. 'Effect' is a direct object, and direct objects are nouns. (think: warnings had what? warnings had effect) 'No' is another adjective modifying 'effect'. 'On my adventurousness' is a prepositional phrase modifying effect; 'on' is the preposition, 'adventurousness' is the object of a preposition (which is a noun), and 'my' is an adjective modifying 'adventurousness'. Sentence #1 is relatively simple.
The second sentence is a little more complex (but not a complex sentence, technically speaking.) 'What you eat', believe it or not, is a noun clause (I think that's what it's called, correct me if I'm wrong), which acts as a noun, and therefore can be the subject, and is in this case. On the technical level, clauses are not ordered in that way, and the word order is switched around to 'you eat what', with 'you' being the subject of the clause, 'eat' the verb of the clause, and 'what' as the direct object of the clause (direct objects can be either nouns or pronouns.) 'can affect' is the verb of the sentence. 'Had' has a very different role in the two sentences. 'Had' is an action verb in the first one and is the only verb. In the second one, 'affect' is the action verb, and 'had' is the helping verb. Then, 'mood' is the direct object of the second sentence, with 'your' modifying it as an adjective.
The two sentences, as you can see just by the lines of the diagram, have different structures and are not the same. Even though 'had' and 'affect/effect' both appear in each sentences, they are grammatically used differently. Long story short, 'effect' is a noun, and 'affect' is a verb, in most cases.
This is what two years of Honors English got me. I hope it didn't go over your head.

Here are the diagrams: