But what about the things I have that only really eat live or frozen stuff? Do I just mix the meds with it while I prep it?
For my very picky Green Terror, I made gel food by adding unflavored Knox gelatine to frozen bloodworms (or you can use any other frozen food they like). I let the bloodworms thaw in the fridge. Then I prepared a Knox gelatine mixture: add 1 pouch of gelatine (7g) to 1/4 cup of cold water and let sit for 1 minute, then add 1/4 cup of boiling water and stir during 2 minutes. Add a little bit of that mixture to the thawed bloodworms (the amount you need will vary depending on how much liquid the frozen food you use contain; in my case, I used a ratio bloodworms / gelatine mixture of about 3 to 1, but you might have to experience to find what works best.) After mixing the gelatine with the bloodworms, add the medication and mix well. Then put it in the fridge for 3 hours. After 3 hours, it should hold together well. If not, you will have to adjust the amount of gelatine in your recipe. Cut this gel food in small bits and feed to the fish. You can keep this gel food in the fridge for up to 3 days.
Do you have some fish that only accept live food? If so, what type of live food do you feed them?
And what about larvae in the substrate, do I just let them continuously infect the fish and treat until there's none left?
Ideally, you should vacuum your substrate. For sand, I use something like this with a bucket, so that the sand doesn't go in the sink: http://ca-en.hagen.com/Aquatic/Maintenance/Cleaning/11062
But my sand is not as small as play sand. I don't know how well it would work with play sand, but it would be worth a try.