Just cycle the tank. Don't turn anything on but the heater and powerhead. When it comes to running media in reactors, that depends what you are trying to address. I love running Purigen on my 55 reef. Then you can go from there. GFO
or some other product for phosphates if you have an issue with them...so on.
In terms of how to run the reactors, you can plumb them into the return line from a sump...but it is best to do in a sump setup with a pump of their own with a ball valve on it so you can adjust the flow for perfect tumble of whatever media you decide to run.