Hey Sasha,
I see your confusion, what you need to do is siphon off any cyno that may be forming on top of the sandbed. You do not need to siphon sand out as well, although even with a steady touch you will probably pull out a small amount. What I suggest is using say a 1/4 inside diameter hose or even a large size piece of airline tubing and gently sweeping over the area.This smaller hose will be less suction and a finer opening to remove only cyno instead of using a large diameter hose that might suck out half your sandbed in one pass. You might even want to try using one of those eye droppers that come in test kits-just make sure it's a clean one! Any sand that you accidental pull out could be washed with RO water and placed back into the tank. Stirring up a little sand when you siphon off that cyno should not cause any major release of organics back into the tank, now if you stirred up all your sand that would cause problems. You only need to siphon when the cyno accumulates to keep it under control.
The cyno will fuel your bubble algae to grow at this stage that's why I suggested adding it to a sump or refugium because you don't want the bubble algae to establish a foothold in your tank whether it's in there for nutrient removal and or cosmetic reasons, you can add a slower growing type of plant after you cyle with cyno has passed and your tank has matured more.
As for cleaning under LR, most reefers don't pull out there LR every 6 months to clean up. Most reefers do however move, upgrade tanks, or re-aqua scape from time to time which helps control the buildup. This is one of the main reasons why some reefers switch to bare bottom. I believe like others tho that sandbeds are beneficial to most reeftanks, however over time if they are not partially cleaned or if there's not enough natural processing going on then they will eventually become unstable and cause a serious problem.
Happy sifting
