By the sounds of it, you want the REC to be a backup source of power, just incase you run out of lava or something goes wrong, because, you will need a constant power supply to keep the AE system going. Because of this, it would be wise to not turn off all your engines, but at the same time, you need the extra engines incase you need some more power. So, I came up with a simple solution, helped with a pic.
Obviously, Magmatic engines on the left, REC in the middle and Rolling machine on the right (simulating where the power is going, be it an AE system or something esle). Basically, what is going on is, the first 2 engines are on constantly, they supply the steady power you need to keep everything going You might need more, depending on how big your AE system is, but the idea is that you have just enough (preferably slightly more) to keep everything running.
The RED in the middle is the backup power for some energy storage, it stores the energy until it is needed and if there is more energy being used than created, it will start to drain. Just so you know, the Conduit on the bottom face is blue and the one to the right is orange, so it has an input and an output.
Next to that is the structure pipe with the gate system. The one by the REC is set to space for energy, emit red pipe signal. At the other end are more gates that control the extra backup engines, the gates there are set to red pipe signal, emit a redstone signal and the engines are configured so that they run if they get a redstone signal. That way, if energy does come out of the REC, it will turn the engines on and fill itself back up.
The problem you were having is that everything was in one line, so energy went into the cell then to the rest of the system. So the REC was never going to be full unless you had an abundance of energy. With this, the REC will only drain if the demand is greater than the supply since energy can get round it and so it doesn't need to drain unless it has to.
Hopefully, that makes sense.