Probably not going to fit, at least not easily. The big difference is the up-pipe and bracket. If you can look at the rear face of a C6 case and a T-19/ZF bellhousing - the C6 has a very smooth case that drops pretty much straight down from the top flange. The manual goes back about 1" and then drops off. The turbo bracket on the manual is a little bit longer and I think the pipe matting flange may be at a slightly different angle to allow the piping to fit around the slightly longer bellhousing. I think the up-pipe is slightly smaller (2 1/4 vs 2 1/2?) to compensate. I haven't actually tried working with a true Banks setup, but I did build the first version of my turbo setup using a Banks C6 turbo mount flange on a ZF5 truck and had a devil of a time getting it to seal because of that offset.
I've never tried exactly what you're saying, so I may be wrong, but I think the most likely way to make it work is to find a mount/up-pipe from a manual truck. Not easy, I know... sorry.