How to fill a div.InnerHTML with Ajax Controls from code behind?

I need to populate a div's innerHTML with some Ajax Controls and <asp: elements (<asp:CheckBox and others). I tried to do this in Page_Load and in Page_Init but it doesn't work, I can put HTML elements but not asp's one. I also tried in Page_PreInit but it is too early, I cannot access the div's InnerHTML yet.

 I could be wrong but I think that putting <asp elements in an InnerHTML at page_load time is too late, these have been already processed (but I could be wrong).

Any ideas or workaround? I could use normal html checkbox instead of asp:CheckBox but the problem is that I need to populate it with HoverMenuExtender (ajax control toolkit) too.
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