In addition to Window > Order (which only seems to allow you to order classes of windows, but that might still be good to keep private message windows away from the rest), if you want to keep things always in the same place, you could...
1. Use a script to connect to networks in order.
2. Use a script to join channels in order
3. enable Tools > Options... > IRC > Keep channels open
and optionally...
4. Tools > Options... > Display > Sort buttons
It wouldn't be the exact order you may desire, but it should give a consistent ordering of buttons.
