No one knows. IRS hasn't released any details about how or when they will make the adjustments.

Since a 1040-X refund can't be direct deposited, I doubt that an IRS-generated refund will be sent that way, six months from now.  But IRS promises of how they can do this automatically are like a lot of things they have said in the past year, then pulled back.  I'll believe them when I see it. 

What they might do is send a notice to taxpayers showing the refund computation and asking for a signature.  That could include a place for banking instructions, but why can't they do that with amended returns?  I may start preparing 1040-X claims after April 15, because I think they will have to work those first.  They have to pay interest, then.