While I haven't read the manual, or am even familiar with your receiver, I am presuming you are using the same source to do both your stereo and HT. I am presuming you have a single connection like SPDIF.
Off the cuff idea is to use another set of connections from source to receiver, namely RCA red/white analogs. Then when you assign/choose that source, set it to stereo, and hopefully that setting will stick with that particular input, while still leaving your HT (optical/coax) at the mch setting.
mmm just an idea . . .
EDIT: ah, I read more carefully. The reason you have no sub when on stereo is most likely because your mains are set to full range. You will have to apply crossover to mains in the receiver setup if you want the sub to play along.
Now, you might ask, how can you get the sub and mains as full range together? Complicated. One way is if your sub has high level I/O, and use the sub's low pass, (never having done that myself), HOWEVER you will have to turn sub as OFF in the receiver to ever get LFE from your movie tracks, and even when you do, it will be GREATLY reduced in signal.
So, moral of the story is to apply xover in receiver for least headaches.