Hi Reeforama!
Many reefers do use carbon on a regular basis, especially if they are keeping critters that may release chemicals or other toxins that would build up in the system and cause problems. It is also useful for spot-cleaning as you did to remove the discoloration of your water. In your case it would probably be better to discard it to prevent the breakdown of the organic matter (yellow color in water) into nitrates. If your water is turning yellow, you may need to examine the stocking level of the tank or increase water changes to reduce the buildup of organics in the water. Carbon is great at removing the symptoms, but it can not solve the problem.
Many reefers do use carbon on a regular basis, especially if they are keeping critters that may release chemicals or other toxins that would build up in the system and cause problems. It is also useful for spot-cleaning as you did to remove the discoloration of your water. In your case it would probably be better to discard it to prevent the breakdown of the organic matter (yellow color in water) into nitrates. If your water is turning yellow, you may need to examine the stocking level of the tank or increase water changes to reduce the buildup of organics in the water. Carbon is great at removing the symptoms, but it can not solve the problem.