What are you using to make the kalk paste ?
Just a cautionary note, a friend was almost blinded when he mixed kalk paste up using calcium oxide in a syringe. The chemical reaction generated heat and caused the syringe to explode. Even using calcium hydroxide, be careful !
That said, once you've carefully mixed the paste, you can shut down all of the pumps and apply the paste using the syringe to the areas you want to nuke. Don't apply too much, as it tends to run down any slopes and you run the risk of having some of that paste run off and land on a coral or invert, damaging or killing it.
Let the kalk paste sit on the target for about 5 minutes to let it do it's thing.
If you've got a lot of stuff to nuke, don't do it all at once. Do 1/3 to 1/4 at a time so you're not messing up your water chemistry using a lot of kalk at once.
When you're done, fire up the pumps and it will wash away the areas you nuked.