How to vacuum soil?

I own a 55 gallon with about 80% Eco complete and 20% crushed coral substrate.
I haven't vacuumed because when I do it sucks up a lot of the Eco compete out of my tank.
So I stirred some of it up this afternoon, and man, it's nasty in there. I have a few plants and plant on adding more one I get a Better bulb, but how to I keep it clean until then?

I stirred but about 25% of the substrate and this was the result

 

Can you attach a chopstick to the end of the siphon (with a rubberband), hover the siphon about an inch above the tank, and use the chopstick to stir the debris up.

 

Above the tank or above the siphon?

I'm oblivious as to whether this "debris" possibly helps my plants or not?

The parts I stirred were not near any plants as I have few now since recently starting API CO2 injection they melted and are growing back greener. But I could do the chopstick bit.

 

Hover the siphon an inch above the substrate and have the chopstick sticking an inch or so past the siphon so it stirs the substrate a bit. Sorry for mis-speaking!

 

Thank you, sorry if I sound overly dumbfounded haha
I just want to make sure I get it right

 

I wasn't clear and I made a typo, so my fault haha

 

I have had planted tanks for a looong time. I have found plants tend to take care of the junk in the soil. The only time I vacuum the bottom is when I up root something and stir up the soil . Once the plant load is established I just hover about a inch over the bottom to suck up any loose stuff or stuff caught in plants

 

Thank you cichlidman
My tank is VERY lightly planted atm as I don't want to add anything that can't survive tetras LED lights. I hope to upgrade later on.
Hopefully then my fish waste will actually be benefit

EDIT: lightly planted as in 3 swords regrowing a melt, some random Betta bulbs recently planted, and some Java fern as a prefilter.
Also some random plants that I hope to ID in the future.