Paul,
I can see this as being a PITA to maintain proper subwoofer levels.
As best I can tell from your description, you will have mulitple cables going to the REL, one as the LFE output from the processor, and two more from the stereo outputs of the stereo preamp.
That being the case, you will very likely need two different level settings on the subwoofer, one as LFE, one as subwoofer in a stereo context. Additionally, you'll need to define front L/R as large so that the subwoofer does the crossover for those speakers in all configurations.
When using the processor for LFE and bass management you should set the crossover to bypass / as high as it will go, unless you have a specific LFE input which does not engage the crossover circuitry. If you do have a specific LFE input, this configuration might work, but I am concerned with how you will manage the (likely) different levels for stereo through the stereo preamp and movies.
It will be difficult, though not impossible to make this work.
Good luck
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Cheers,