Heh, it confused me so bad at first to. I'll do my best.
So. First thing's first. You need the pokeradar. You can't use it on a bike, so make sure you're walking. Also, it helps a LOT to have the radar registered.
You will also need lots of repels. I find it usally takes about 40-50 Max Repels to get to a chain of 40, but it's always best to have at least 100.
And remember, Quick Balls are your FRIENDS. 8D
The first thing you need to do is decide what pokemon you want to chain. I mean, it doesn't HAVE to be the first thing, but it helps. Remember that you cannot chain pokemon that are only found in water/caves/Safari game. Only pokemon found in grass will work.
Then, go to where that pokemon is located, and try to find the biggest area of grass you can find. The best are the ones where you can stand in the middle(ish) of the grassy area and count four squares of grass in each cardinal direction. A great example of this is the large patch just above Floaroma Town, right before the Eterna Forest.
When you are trying to start a chain, it's usually good to stand in the middle when you activate the radar. Four patches of grass will shake, one in each "ring" of grass around you. Which means, the first patch from you makes one ring, the second patch away from you is in the second ring, etc. These can either shake slowly with no added effects, shake fast with yellow lines that indicate rustles, or the can shine brightly twice, without shaking at all. The last option will always be a shiny.
Now, once you've started a chain, you want to go for patches in the fourth ring-- the farthest ones away. Remember that if these fall on the edge of the grassy area, are behind any obstacles, or touch any object, it would be better to reset. To reset the radar, just walk 50 steps and use it again to get a fresh four patches.
People have different ways of doing this, but here's mine: if you are in a patch that has exactly four rows when you stand in the middle, run to reset in the third row away from the END of the grassy area. Keep resetting until you see a grass shake in the third row away from the end on the other side. That ensures that it is four patches away, exactly.
Also, it's easier to chain the normal-shaking patches than the fast ones. They're easier to see, in my experience.
Once you get your chain up to 40 (may take a few tries, Poketch App. 20 helps keep track), then good, you're at the checkpoint. For some reason, this number is when the chances of finding a shiny increase to something like 5%.
Now, once you get to 40, don't look for your regular patches anymore. Just keep resetting (and resetting, and resetting, and resetting...) until you see a shiny patch. This can take anywhere between two resets and hundreds of resets (though rarely that long), depending on your luck. Once you've caught your first shiny, save, then continue until it breaks. =]
I know that's not the most comprehensive guide. Is there anything you still don't understand?