Sweet!! Glad to see that he is all better! What I would do is monitor your ammonia, if you see a spike grab some ammo-lock. With a new tank it is going to have a little bit of ammonia and thats ok, it will eventually disappear. I would definitely stick with the flakes if he is eating that, you could do mysis a few times a week if you wanted.
I have found a way to feed mysis that actually works out pretty well. Because you only have one fish in your tank at the moment, you realistically only need about 1/4 of a cube of mysis, thats the MAX. Anyway, cut 1/4 of a cube off and put it into a clean cup. Mix in some saltwater and stir. Next, get a syringe and suck the liquid out of the cup and the mysis will come with it. Now that you have your concoction of mysis, INVERT the tube so that the tip is vertical in the air. The mysis will sink away from the "open end" of the syringe. Simply drain the water out and this will eliminate some of the small pieces that your clown wont eat and that would only add to the ammonia. Now suck some saltwater back up and feed to your clown. Squirt one shrimp in at a time so your clown can get all the shrimp and this way none will be wasted.
Thats the method I use anyway, its better than dropping a frozen part of a cube in the tank or just simple squirting in a ton of shrimp. Doing it that way will be quicker, but the amount of food that the clown will miss will only aid to ammonia.
I feed frozen food like three or four times a week, brine shrimp two or three and pellets the rest of the time. I like to vary their diet a little bit. One thing about the brine shrimp is you definitely need to suck them into a syringe and then DRAIN the water out of the syringe. This basically removes the crap water from the brine shrimp. Suck water back up into the syringe and feed the fish one or two at a time. When you get more fish, you can shoot three or four at at time to make things quicker. The reason your dont want to add water from the brine shrimp bowl to your tank is that the water in the brine shrimp bowl is super high in ammonia. The water just skyrockets in ammonia because of the dying brines, their fecal matter, and no circulation/filtration. This is just another way to keep your water levels in check and keep your inhabitants happy
If you get a chance take a pic of your set up and clown!!!