I rencently moved and unfortunately lost my favourite fish (my 16" Tiger Oscar named Wolverine) After much discussion with my young kids we decided to move their 2 year old goldfish  "Goldie" ( I have yet to figure out what kind it is) from its 30 Gallon tank to my 90 Gallon Oscar tank. The tanks was cleaned and set up correctly and Goldie has been happy in it for a week. The kids wanted some feeders since there were so many different kinds in them I agreeded as the extras will become snacks for when my new Oscar tank and Piranha tanks are finished. I use a liquid water test kit that matches to colour coded cards been using it for 7 years and have never had a miss read plus it is easy for the kids to understand it if it good or needs fixed. I went to my local lfs which I have never had a problem at in the past and bought a 100 feeders none bigger than an inch so they would have some room to swim  and grow while I overhauled the 30 gallon my 2 10 gallon isolation tanks my other 90 gallon and my new tank. The feeders took to the tank with no issues all came up to the top after a few hours and swam along the bottom what seemed in search of food. They were fed a small amount and as always extra was removed. 12 hours later I had to leave for work so I did another water test and all came back good. Nine hours later I got home and found about 20 fish dead and about 60 covered in white fluff ( i presume to be ICK) I tested my water and all reading were still good. I treated with ick treatment and aquarium salt did a 25% water change and went to talk with the lfs this morning they sold me some more meds and told me to resalt the aquarium. I have lost another 20 goldfish but now it seems to be under control and the remaining are doing ok. I still expect to loose 6 more that look pretty bad right now but the rest should surrive. What I do not understand is why are the readings still normal? Tonight the nitrates were a little up I did another water change and a few hours later things were back to proper readings.

I figured as much but like I said this lfs is normally pretty good.     As for my water I had my oscar for 7 years so i am used to lots of water maintainance.

By the sound of it, these fish simply got stressed from the change. Moving is very hard on a fish, especially one that already is carrying all kinds of nasty disease, like feeder fish do! Next time you get them, like nabi said, quarantine and preventive treatment may sometimes work, but you should consider most of them pretty sick and not be very surprised if they won't make it.
Needless to say, feeding these to your piranhas and whatnot would be another contamination risk.

In the end it really doesn't matter what size the fish are at the point of stocking, they WILL outgrow the tank sooner or later, so really, when it comes to commons/comets, nothing more than 1 fish per 20 gallons of water.
I'm aware that you were going to let most of them be food for the piranhas, but still, good thing to think about

Oh if its piranha food....

Thats what I thought the nitrates had gone up to 25 but I got them done quick with a few water changes alas Goldie did not make it....

Meds? Are you using something that's interfering with the biological system in the tank?
That usually causes the tank to have problems with cycling for a pretty long time, and that in turn makes the environment that much more dangerous for the fish!

So the only problem with the water quality is the nitrates? Are your fish still showing symptoms of infection?
I would actually think of the good of the tank and simply start removing the meds asap if the goldfish don't show any obvious symptoms. Do some large water changes of about 50-75% to get rid of the medicine when that time comes.

I wouldn't ever treat such a huge system in the first place, imagine that you have to use pretty many big doses of medicine.. It's better to get a fish every once in a while and quarantine it (or two) in a 20 gallon tank or along those lines.

I think no matter how good a pet shop is in the end, there's always a risk, and especially with feeders, they're always neglected :/
But in any case, it'll be nice to see it all set up and ready