You can move the DX wrapper window by positioning your mouse at the window's top left corner. Then click and hold as if you wanted to move a standard Windows window. Your cursor will disappear, but you should be able to move the window. However, you can only move it 640 pixels from the left corner of the screen. Depending on your desktop resolution and game resolution, you might not be able to move it all the way to the right.
You can also use another application (like Borderless Gaming) to specify a position where the window should be.
If you're using another wrapper (Strangebytes ddraw patch or cnc-ddraw wrapper), you can move the window after you enter the game. Simply pick Single Player or Multi Player, pick your character, then move the window without any limitations.