1. I could not think of a better short name for what I just called "Element ID"... it is not for the active_menu id... but when set to yes it will add an id to all elements which let you design each element individually. The consequence is that there will not be the active_menu id anymore because only one id can be assigned. Currently there is no option to turn off the active_menu id... is this important?
2. Yes. Could probably even use SQL to change it and execute something like (untested):
UPDATE mos_menu SET type = 'mod_exmenu' WHERE type = 'mod_mainmenu'
If you want to change the default menu module to use you could hack the Core...
/administrator/components/com_menu_manager/admin.menumanager.php line 189 (Joomla 1.0.2)... change it from:
$row->module = 'mod_mainmenu';
$row->module = 'mod_exmenu';
But with the split menu capability you may not need that many individual menus and menu modules anymore. (Which would maybe even improve your pathway)
3. I may better direct you to the following thread: http://forum.joomla.org/index.php?topic=9977
If you set "Active Menu Class" for both to "Yes" then they should show for both... the split of a menu however requires you that both menu modules use a single menu... but the top shows for example the first level of your menu and the left menu shows all other starting from the second level.
Btw. when adding "Active Menu Class" I think I forgot something... thats why I will probabably add "mainlevel_current" and "sublevel_current" for the item which also gets the active_menu id. So if you are creating your CSS you could just add them as well already.
I hope that explains it a bit better.