I have a nano, when i acclimate something I just mix up a batch of new SW and start the acclimation, as i take water out and put it in the bag, there will be less water in the tank. By the end there is a lot less water in the tank, and i just use the new SW i mixed up and make the whole thing into a water change basically. That way i do a water change AND acclimate my new addition. Just make sure the new SW has the same temp. and SG as the tank and you'll be fine.
If anything just cannot go wrong, it will anyway.