I don't understand why you didn't make the soffit flush with the duct work. Nevertheless, I see your issue.
I think you will have to take out the existing registers and cover the holes with metal and then pop-rivet the covers in place. Cut new holes for duct work extensions in the new covers (6"? 8"?) and then install take-offs and your extensions as required. Carefully seal the new seams with foil tape.
I note you do not have the duct work insulated. I presume this means you only run heat (not A/C) thru the duct work. If you do run A/C thru it, you really need to insulate the entire duct work system before you enclose it. Otherwise, if/(when?) condensate forms, it will eventually ruin the material you make the soffit out of. It will be FAR cheaper and easier to go ahead and do that now, than in the future.
(As an aside, I am not sure "Soffit" is the right term for this--it could be a regional thing. I would call it an HVAC chase.)