I would also look at the SVS PB12-Plus subwoofer. It's close to the same price as the REL T9i. However, it is significantly heavier/larger (cabinet bracing) and will play a lot lower. I don't know how the REL vs. SVS really compares, but I would lean toward the REL for power overhead and low bass. Just an option. And I also think that getting two subs (of whatever model) is better so that they each supplement the left and right channels individually. There aren't really any timing issues to consider. However, some subwoofers will have a phase adjustment to help with blending.
You could hook the subwoofer to the high-level output of the amp, but the signal still has to be converted back to low-level before it enters the subwoofer amplifier. If it were me, I would just use the RCA output of the Krell KRC-HR. The KRC-HR output impedance is documented at 5 ohms (which is insanely low for a preamp). Your FPB400 has an input impedance of 100k ohms (it is very high which is good). This means that you will not have any problems with the preamp driving two different amplifiers (the FPB400 and the subwoofer inputs). The impedance can be an issue if the amplifier impedance is really low (like 20k ohms) and it is driven by something like a tube preamp. I would just use a nice large awg solid-core interconnect such as the Beldon 1695A coax subwoofer interconnect from Blue Jeans:
https://www.bluejeanscable.com/store/subwoofer/index.htm
The larger 18awg solid-core conductor will transfer bass frequencies extremely well. You do not need a super high resolution cable for the sub. In fact, going to a higher resolution interconnect that will have smaller awg solid-core conductors may actually produce weaker bass waveforms.
In your situation, since you have bass nulls at the listening position, I would not implement a high-pass crossover for your Apogee's. You should still run the Apogee at full range so that it is outputting as much bass frequencies as possible. Then place the two subwoofers as far away and as far into the corners as possible. This will give you multiple distances where bass frequencies are generated and help reduce the bass nulls from waveform cancellations (when they bounce off the rear wall and come back).
While this will definitely help with bass resolution, keep in mind that you may still end up having to do some acoustic treatments for the bass frequencies (such as GIK bass traps I mentioned above).