Resizing one window should not change the size of other windows unless you are on the Windows OS and have windows maximized. Creating a new window or resizing an existing window will drop your windows out of maximized state. This leaves you with several choices for working around this problem:
1) Don't operate with windows maximized. This can be a problem with having two sets of scroll bars--one for the application window and another for each FileMaker window opened within it.
2) Write scripts that modify the sizes of existing windows after opening/resizing the new window. This does cause an annoying "jump" to the windows but careful size settings that pop the unmaximized window back out to nearly the original maximized dimentions can minimize it.
3). Don't open a new window. Use Freeze Window to keep the current window unchanged, switch to the other layout in the same window. Process the records or whatever you neeed to do and then return to your original layout.