If you are following Step 12 of the instructions on https://github.com/LavishSoftware/ISBoxerEVELauncher, then InnerSpace should be loading the games up in the Window Layout you set in your profile.

If you are selecting the default profiles from the top of the Inner Space right click Menu, or in the ISBoxer EVE Launcher, and clicking on the button Launch with Inner Space, then you wont get the Window Layout set in your profile.