Many (but not all) programs support the -geometry option. For example, with Netscape, you can call it with
netscape -geometry=0,0,400x600
and it will start in a 400x600 window, with the upper left corner at coordinate (0,0). (You may want to check my syntax on that - I'm stuck at a Windows box, so I can't check it right now.) Telling a program which desktop to start on is a window manager specific thing, so unless you're using AfterStep, I can't help you on that. You'll have to check your documentation.