I am confused a bit about the vacuuming of the substrate though. I have a planted aquarium, gravel substrate and vacuum the gravel in some of the area that is not directly planted. Am I not doing a thorough job? I thought that the plants needed some of the fish poop etc to help them grow. I also fertilize them once week with Flourish Comprehensive. Could someone clarify this just a bit more.
I no longer touch the substrate in any of my planted tanks. At one time I did what you suggest, even recommended it. No harm in that process, but I think it may be best to leave it alone, if you have substrate-rooted plants. By these I mean plants that root in the substrate--swords, crypts, aponogeton, vallisneria, sagittaria and so forth, and stem plants when actually rooted in the substrate.
The reason is related to nutrients. Fish waste, excess food, plant matter, dead bacteria, dead fish, etc. are all organic matter. This stuff settles on and works its way into the substrate, or it should in a balanced aquarium. In the substrate, bacteria break down the organics, with the help of snails that break larger bits into minuscule bits that the bacteria can more easily handle. Plant roots release oxygen for the aerobic bacteria, and more oxygen comes down in the water; the bacterial action warms the substrate and water, causing the water to rise back up into the aquarium where it naturally cools and then is pulled back down with the thermal currents. [This was the principle behind using substrate heating cables that became popular a decade or so ago, but without other high-tech devices it is best to let nature do this.] The water also brings down other nutrients that the plant roots assimilate, along with those produced by the breakdown of the organics. Removing any of the organics from the substrate is removing essential nutrients, but the best is yet to come.
All this bacterial action produces copious amounts of CO2. There is far more CO2 produced by bacteria in a healthy aquarium than all the fish and plants combined (fish and plants produce CO2 during respiration). This CO2 is a vital plant nutrient. This is the thrust behind soil substrates; they encourage bacteria more and thus create more CO2, in theory anyway. The truth is that there is very little difference, but I won't get into that.
Most of the afore-mentioned is aerobic, utilizing bacteria that need oxygen. But there are also anaerobic bacteria that either do not need oxygen or can produce their own. These are also very important for the health of the substrate and the aquarium. "Dead spots" are necessary, we just don't want the entire substrate becoming one. But having spots under rocks or logs that are anaerobic is beneficial and will contribute a lot to the overall health of the aquarium. Denitrification occurs, converting nitrates back into ammonia or more likely ammonium (in acidic water), another essential nutrient.
So, leave the substrate alone if you have substrate-rooted plants. Provided that the aquarium is biologically balanced, meaning the fish load is not greater than what the system (plants, water volume, substrate) can handle, you will be fine.