1. replace variables $HEADER and $FOOTER (to rid warning about using deprecated headers and footers).
Each custompage's header and footer needs use different variable name (in my case $OLDFOOTER01, $OLDFOOTER02, but header is the same for all pages, so just $OLDHEADER)
2. add new headers and footers for version 2
$LAYOUT['_header_'] = '';
$LAYOUT['_footer_'] = '';
If you have one version of header, you can use it directly.
3. add new layouts (according theme.xml)
add $LAYOUT['default'] with {---}
add all needed layouts according theme.xml
add correct footers
Menu manager is now fixed.
Important: Check if Go button displays Menu areas, if not, something is wrong.
This is new in version 2, each layout has the separate set of menus.
Warning: Be sure that you set correct default layout in Theme Manager at the beginning. If you change it later, you will do this again.
Just check what menus are used for default and add the same menus with the same config for new layout.
Be sure you are on the correct layout and be aware that menu left checked after you add it to layout, so without unchecking you add it again with new menu.