Try this:
To control the size of primary and secondary IE windows, start by closing all IE windows. Then launch IE, right-click on any link, and choose Open in New Window. Size the secondary window the way you want all such windows to be. Now close it by clicking on the X icon at the top-right corner while holding down the Shift key. Repeat this for the primary window that remains. You may have to repeat the process from time to time.
Good luck!

Mike