Howdy,
Well, (sic) it really doesn't make much difference.
Chemically speaking, You would remove maximum minerals(and salt) from your cooling system if you flushed with distilled water since you would be flushing with pure H2O with NO dissolved solids minerals or salt.
If you used water that was saturated with minerals or salt (or both) you would not remove as much except by the mechanical action of the water.
now having said all that

, It probably makes little or no difference either way.
If you operate in saltwater , you should use something like Salt Away
http://www.saltawayproducts.com/EngineFlushPage.htm or similar product.
Cheers,
Rick