What are you having problems with? Are you using a feed pump to add water to the reactor or are you using the siphon method to add water to the reactor? This is how I set up my reactor:
Basically what you want to do is add your media to the reactor, and then get the reactor running so there is a constant stream of water entering your tank from the effluent line of the reactor (on top of chamber). You then can turn on your CO2 but start out with a slower bubble rate (maybe 30 bpm or so). Using your control valve on your effluent line, dial it back to where it is just under a steady stream, a fast drip is ideal. I shoot for an effluent pH of about 6.5 or so. Now you need to test your tank so you can get your reactor dialed in properly. Monitor your calcium and alkalinity levels over a period to determine if they are remaining stable, are too low, or are too high. You can then adjust your reactor accordingly by adding more or less CO2 or icreasing or slowing the drip rate. After a short time you will have your reactor dialed in perfectly for your tanks requirements.
Hope that helped.
Brandon