I've tested my demo site (http://c5extras.com/add-ons/mega-menu/) on my iPad and it works fine. If there's a layering issue it's likely to be an issue with your template. The most common causes would be:
1) Z-index is too low;
2) Position:relative is required on a DIV tag that wraps the menu

Both of these require some reasonable knowledge of CSS. You can confirm the template is causing the issue by setting your page theme to the default "plain yogurt", and if there issue doesn't persist, then it's the theme.

Otherwise, if you have some kind of slideshow block below the menu, that block could be causing the issue (the above 2 suggested fixes should work though).

Hope this helps.

JB

Hi JB

The thing is that the header should be fix on one position. When I change that, then navi is working fine but also not fixed on one position.
I tried to add a Z-index but wasn't really success full.
Is there an other way?

Thanks

Ah, I see. The problem is that mobile Safari doesn't have built-in support for "fixed" positioning. This isn't a restriction by the Mega Menu add-on. Rather, it's a well known design "flaw" in Safari. It is very annoying for many web developers, but there isn't much that can be done about that unfortunately.

I was afraid of this answer …
Thanks