2 channel and HT set-up?

[GHW]

Hi All,

I have question for those of you much more up wth the whole HT thing than me ( ie probably everyone)
I'm putting together a HT but wanting to incorporate 2 channel as this will be used most of the time.
I'm planning on getting a reciever with pre-outs, going from the main outs into a Linn Majik Dsm hdmi which can apparently have one of the inputs selected for HT bypass? this will go to my main amp(s) yet tbd but something to drive some newly aquired Wilson Sasha's.
My idea was a sort of " cake and eat it to " by having everything bar the Linn, amp(s) and sub switch off for two channel then everything else switch on and use the lfe out to power the sub which is a Martin Logan Depth i with capability for using more than one input.
This will all be controlled by Control4 automation so there's no problem with switching etc to achieve this.
The thing I can't work out is the conflict with lfe and another input on the sub if the Linn is being used in both systems?
When in 2 channel this will be no prob but when in HT both the lfe and rca or speaker input will recieve signals so surely will cause a problem ? any ideas how to get around this or will I be forced to just not use the sub for 2 channel listening? any suggestions would be most welcome.
I haven't decided on the other equipment yet relating to the HT bar the screen will be screen innovations.
cheers for any suggestions how to make this frankenstein system work !