It appears that mIRC does differentiate between DCC and query windows of the same name and on the same network.
The only thing that I found that would make a difference (without waiting for an update), is to use the /queryrn command for the query window. This will allow you to change the name of the query window, but it still goes to the correct person. For example, if I had both DCC Chat and query windows to Zyxak, I could use /queryrn Zyxak Zyxak_PM
This would make the Query window called Zyxak_PM, and the log would be named the same.

Regrading the windows positioning..sorry, no help there.