You can refer to windows by name, so from your child window, just have your javascript access your form object(s) underneath this main window. I'm no JavaScript expert, but instead of doing something like this:

myform.inputvar.value = 'whatever';
[download]

do

mainwindow.myform.inputvar.value = 'whatever';
[download]

or whatever other objects you have to work with between 'mainwindow' and 'myform'. You may wish to consider consulting any of the thousands of JavaScript-oriented web sites on the 'Net for information on accessing objects in multiple windows.