Re: I have trouble with the greenhouse effect as pertains to earths atmosphere?

This is an old problem. Basically, if you think of the atmosphere as a single sheet of material, your objection applies, because additional carbon dioxide or water vapor will not alter the amount of radiation passing all the way through the sheet. However, the atmosphere is in reality a multitude of layers, all with different concentrations of gases and water (higher concentrations near the surface, lower concentrations aloft). If we take all of these layers together, we find the net result is that radiation in the absorption bands of CO2 and water vapor cannot directly escape from the surface into outer space. However, to understand their effect on the atmosphere, we must consider how far up do these rays penetrate, and therefore, how much are they delayed in reaching outer space? The greenhouse effect is often described as heat "trapped" in the atmosphere, but it is not permanently "trapped," it is merely delayed in its progress back into outer space. Because every day there is more energy coming in from the sun, the "delay" in returning energy to space makes our planet warmer.
You can find a good explanation, requiring a little bit of science but mostly just some thinking, here at RealClimate. Note this article has a "Part II" with a more technical explanation. The bottom line is this:

• (a) You’d still get an increase in greenhouse warming even if the atmosphere were saturated, because it’s the absorption in the thin upper atmosphere (which is unsaturated) that counts
• (b) It’s not even true that the atmosphere is actually saturated with respect to absorption by CO2,
• (c) Water vapor doesn’t overwhelm the effects of CO2 because there’s little water vapor in the high, cold regions from which infrared escapes, and at the low pressures there water vapor absorption is like a leaky sieve, which would let a lot more radiation through were it not for CO2.