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Yeah, you can do it, but my experience with Bose is that it will sound less than optimal with aftermarket HU. But maybe things have changed.
What HU and sub are you looking into?
I just put a Kenwood single din in, with a CB stacked on top (modded a dash kit so both would fit flush). I use my iPhone & AUX jack to do everything anyway, so I scrapped the DD idea for the CB combo. I'm really happy with the outcome.
As for sub, I'm planning on JL. Either a 10 or a 12. They've never let me down. Great sound with minimum power and air space. I just have to figure out where to hide it all.