You can just add the meds/vitamins/supplements to the water the same you would if it was a normal waterer. If you're only treating for a little while, and your water system is large, then just don't fill it up all the way, and not too much water will be wasted. Or, you can set up a temporary watering system in the form of a normal waterer or plastic cups, and then go back to the automatic watering system when the treatment is over. I've used both methods before; both work fine.
As for preventing mold/slime from building up, I use a disinfectant known as Oxine to do that. You put 1/8 teaspoon Oxine (it comes in a huge bottle that lasts a long time) per gallon of drinking water. Even in the summer heat, I rarely get algae growth in my waterers as long as I use Oxine. In the dosage used, it does not hurt the birds drinking it, either.
