Changing Window Size in Baseball Mogul

Yes. You probably already know that you can resize the main window as you can with most other apps in Windows, by clicking the minimize and maximize buttons in the upper right, or by grabbing the lower-left corner and dragging it until the window is your desired size.

However, I assume you're asking about the dialog boxes (aka "popup windows") such as the Lineup, Defense, Bullpen, Sortable Stats, etc. To change the size of dialog boxes, go to Options on the Tools Menu and change the setting for "Dialog Box Size":