If you use the StartMyDay controller, there is a provision for managin the window locations based on a property of the adapter named "StartMyDayControl". Set this to the "form" you wish to position and then in the dialog from the Start My Day Controller, you can save the position of apps. Once saved, they'll startup again in that position. For Internet Explorer, you'll need to add the outermost IE Window control from the "Windows" controls tab to your adapter.
If you'd like to do this on your own, simply get/set the Location property of a given "form" control to place it wherever you'd like.