Not sure what you mean by "not on top level". Maybe you mean it is not behind other windows? If so, this is probably a consequence of the focus stealing prevention behaviour setting. Which window manager are you using? (e.g. Gnome or KDE - but might be others).
There are cdsenv settings to control window sizes. Put something like this in your ~/.cdsenv (adjust the coordinates to suit your needs):
layout leWindowBBox string "((120 185) (1020 875))"
schematic schWindowBBox string "((120 185) (1020 875))"
schematic symWindowBBox string "((120 185) (1020 875))"