1) Theres a Move/Resize Window script step you can use to specify the location and size of any window currently open. You can include this step with a script that runs when your file opens to set the original window to a specified size and position. If you then use New Window commands to open additional windows, you can specify the size and location of the new window in the parameters of the New Window Script step.
2) That appears to describe the opposite of my own experience with windows in FileMaker. If the Scroll bars are inactive, it's due to the window showing all the needed space for the current layout. To get the scroll bars to be active, I have to resize the window to make it smaller--not larger.