I thought using a clear cup would help too, but when i experimented they FREAKED. Opaque is definitely the way to go.
This is how I suggest doing large water changes:
To do a water change, use a little cup like a plastic solo cup - this cup must be only for him and have never been used with soap or other chems. Scoop him up in this cup (keep him in the cup about 1/4 full of water - it doesn't need to be much because he won't be in it for long) and leave him in the cup while you change his water. To do the 50% use a turkey baster - dedicated only to him that has never seen soap or chems - and drag it through the gravel and try to suck as much of the poop out as possible, in addition to 50% of the water. Use a thermometer under the running tap to get it to be the same temp as the water that is normally in his tank. When the thermometer says the flowing tap is the right temp, fill back up his tank. At this point, add the conditioner (dose for how much water you change - if you change half the water you add half gallon worth of conditioner, If you do a 100% water change dose for the full gallon change). Float his plastic cup with him in it in the new water. Slowly add a couple tablespoons of the new water into his cup every 10 minutes for at least an hour. Finally, dump him in gently but try to get as little of the old cup water back into the tank as possible. When you do the weekly 100% you will do mostly the same thing except empty his tank fully and rinse everything in it very well under warm water but never use soaps or chemicals. Once it's fully cleaned/rinsed you can refill it and repeat the cup/acclimate phase.