You can do this with a batch file. The sequence editor window settings are stored in the registry at
HKEY_CURRENT_USER\Software\National Instruments\TestStand\<VERSION>\GUIs\Sequence Editor\Settings
where <VERSION> is the version of TestStand you are using (2.0, 3.1, etc.)
Start the sequence editor and set up the windows to the positions you want to restore and exit the sequence editor. Use the registry editor to export the above registry key to a file (say "seqeditsettings.reg"). Then create a batch file that contains the following:
regedit /s seqeditsettings.reg
seqedit.exe