The VB is where it get's messy, because there is no way to get the fluid out that sits on top of it!! But simply flushing the trans fluid shouldn't be a mess at all. Did you shift through the gears like you were suppose to? With my 6.0 cooler mine holds right at 20 quarts so for me that would mean I still had a gallon of old fluid in there and I would never settle for that. Not sure why you didn't pump another couple quarts through it for a full flush. Your trans isn't going to die from this, you should be fine but it's not ideal.
You'll be okay.
NCH