Hmmm, I don't know why anyone would recommend that.
If you read through the threads here, you will see a lot of different views and opinions on substrate. There is bare bottom, shallow sand bed and deep sand bed. By mixing the substrate as you have there, you've got a shallow sand bed on top of a shallow sand bed. Now assuming that the fine sand is 1 inch deep, you will have some nitrate reduction, but this small amount of sand with a different size grain on top will eventually lead to a crash of your bed. I can't say exactly how long that will be since I don't know how much livestock you keep and how good your husbandry is.
The reason you've got the green layer is probably because the first layer is releasing some of it's nutrients, but they are getting caught up in the layer above rather than precipitating out of the system. Also, as you mentioned, there is crud building up in the top layer which is also building up nutrients.
Increasing water flow just above the sand bed may help keep things from settling in there which will give your protein skimmer and water changes a chance to remove some of the nutrients.
I'm sure the last thing you want to hear is that I would either go with one grain size or go without sand all together. The idea of sand removal will make you want to choke someone... probably me since I'm telling you that that is what I would do.
Bare bottom (BB), shallow sand beds (SSB), and deep sand beds(DSB) are all methods in keeping fish tanks. All methods are used on this site. All methods are highly debatable, argued here frequently. For example, Solbby is a BB guy, Chiefmcfuz is an SSB guy and I use DSB. Others have either BB or SSB and run a remote DSB like House of Laughter. None are right or wrong. You just have to make sure the rest of you equipment and husbandry skills can handle the different methods. Search this site. There are plenty of threads on the BB, SSB, DSB topic. Try not to get too wrapped around all the links posted, unless you feel you understand them. Most of the time, I can't. Read about it and as you get closer to a decision, PM guys who use the method you like better.
Hope this helps. BTW, I'm also not saying that what you have won't work. You are experiencing a common problem that many do who mix layers of grain sizes which tells me that this is not a very good method. There have been a few guys who have come to the site recently with the layers sand bed and it didn't seem to be working out for them either. I believe I've seen this method mentioned in an old Martin Moe book. While that book may have been ahead of it's time, that method seemed to die out many years ago. Either way, good luck.