As I have said many times in here- I am still pretty new to the art of building a computer into a car but I've been building computers in other things (sometimes regular cases) for years.
Using 2 separate power supplies in a computer was actually not uncommon a few years back: when scsi and then IDE RAID became somewhat popular with hobbyist types, but power supplies were still small. Add overclocking to that, and the need for many fans at times....
And connecting the green and a ground was the way we did it- soldering for a permanent connection, or with part of a paperclip for temporary use.
I do not know any reason to think this would be a problem in an automotive environment- you'll still have ignition power to turn the unit on/off, so won't drain the battery.
Should be fine, I'd think.



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