I do the same with arm media in the main chamber and zeovit mag stones on the secondary, with the rx6 you get n extra chambe which I like to fill it with either reborn by two little fishes or DD brand of fine media. I figured it's always good idea to have a variety. One thing you have to watch out for is to make sure the main chamber is filled with corse media and nothing else or it might make the recirculating pump fail prematurely.
As for the effluent, first I would hook up the ph probe and set it to 6.5-6.7 so it will activate the solenoid once it goes over the desired ph value then I would test your water parameter(I usually keep a log on all my testing but I have been lazy and the wife is doing it for me
). Now start the effluent at a drop or two pre second depending on how heavy your tank is stocked. It is very important to test and retest your water for the next week or two so you can dial in the effluent rate. Then it's pretty much hands off. I do check my kh once or twice a month just to make sure I am still on point, not until my corals started growing rapidly that I noticed a decrease in my alk and calcium but that was easy as a turn of the knob to increase the output. Since you have the ph regulated, it will automatically accommodate and raise up the bubble rate.
One last thing, I do run a feed pump for the intake instead of using gravity. I like the idea of a low pressure feed pump cause it will always keep the reactor circulating and at the same time prevent it from clogging. It does put a little more pressure on the oring seals but I am confident on those silicone orings will hold up just fine.
Let me know if you need more help.
Rich