Sand does not really absorb broken down waste very well. The trick with cleaning sand is to sorta create a slight current with your siphon that raises the detritus up off the sand bed and then you vacuum it up. If you actually dip the siphon into the sand bed, you will quickly be vaccing up more than sand than waste. A powerhead lower in the tank than you would normally put it will also help keep detritus off the sand bed and kick it up into the water column to be filtered out.
If you have capped with sand, I would be especially careful not to suck disturb the sand bed.
If the Eco-Complete is on top, I would only siphon up excessive waste. Eco-Complete has a lot of capacity for taking in nutrients, supposedly.