Question about Transplanting.

So i built my areo system, I have an 18 Gallon tote, i have a 14'' air stone and a 8'' air stone, a pump that is for 60 to 100Gallon tanks.
I had to get pea gravel because i couldn't find any clay pebbles. I also couldn't find any baskets so i used drinking cups. I will post pics later.
My question is this.
I have some seedlings that were started in soil and are now 2-3'' tall, I want to transplant them to the new system. DO i still bring the water up to 1'' in the bottom of the cup or more? I also used Miracle grow all purpose flower food. I'm going to get this all set up today but want to make sure in clear on the water level first..


\thanks

Can anybody help me out on this????
Is miracle grow ok to use? should i mix it at 1/4 strength?
i have 12 gallons in the resv but its mixed for 10.5gallons. the plants were planted on the 25th and i moved them sat night. the roots were already in the water once i moved them because they were already long enough to reach.
Is miracle grow to strong? and would 1/4 strength be good enough?