Can anyone please advise which file controls the pagination codes, as it's stick to top than showing below: http://carnity.org/classifieds/?page=3

I want it to show below like here: http://carnity.org/classifieds 

That’s not a problem of the pagination, but of your content elements which are set to float. You need to wrap them with the CSS class ipsClearfix, so the floating stops after the last floating element. 

Thanks Ralf, sent your reply to programmer and got it fixed. :-)