If you bowl him and add the sand and it's cloudy, just siphon off the cloudy water and refill carefully, it should be clear then. Be sure to thoroughly rinse the sand ahead of time to get as much of the dust and really fine particles out first, this helps a lot.
I neat trick I saw used is to use plastic bags for the water. You can fill the bag, put it in the tank and release water slowly while fully controlling where it goes. The next bag is even better as you can submerge the bag somewhat and just remove the bag leaving the water in place without any flow.
If the water is at temperature then there is no reason that you cannot just put the fish back in the tank.... cycling and plants are other considerations though.
In such a small tank you definitely want to take the fish out to switch substrates. In a large tank, you do not have to, though if you are new to doing substrate switches you probably should. I removed my fish the first couple of times, but then left them in every other time. If you wash the sand well enough, it won't be cloudy. If you wash the sand well enough, there's no reason to leave the fish out of the tank for any longer than the switching process takes. If you wash the sand well enough......
Do yourself a favor and wash, wash, WASH the sand, then wash it again. Put the sand in a 5 gallon bucket, fill it with water while swirling your hand through the sand. When the bucket fills up, take note of the water. Is it clear? Can you see the sand on the bottom? If not, pour out the water, and start again filling the bucket and swirling the sand with your hand. Do this as many times as it takes for the water to be clear once the bucket is filled, and for you to see your hand on the sand. THEN, the sand will be clean enough for you to add to the tank and not cloud the water. I put the sand in a pitcher with a cup, sink it, then pour it out on the bottom to deposit the sand. For such a small tank, just scooping the sand out of the bucket with a plastic cup, sinking it, and pouring it will be all you need to do.
Some people advocate the bottle method of cleaning sand - the assumption is that the sand is clean because the water is not clouded. However, once the sand is disturbed, it will cloud the water. 20 fluid ounces just isn't enough water to properly clean the sand, as you will see if you use the bucket method I outlined. The bottle method is a a terrific method for DEPOSITING sand, especially in tight areas, or in small tanks. You would just need to wait for the sand to dry before filling the bottle.
Now, are you going to disturb the sand that much in the tank? No. But, CLEANED sand won't cloud the water, even if you do. And, that wasn't a lot of sand...
Cloudy water from not cleaning the sand well enough is not the end of the world - your tank won't explode. It's just annoying, and completely preventable. You may find thoroughly cleaning the sand is more annoying than the cloudiness. If that's the case, then the bottle method is for you. However, know that you might end up with cloudy water after each water change, for quite some time - depends on how much the sand gets disturbed when you add the new water. Cleaning the sand in a bucket, as I described - the sand will never cloud the water.
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