I have some posts which do not have any category, by default, wordpress shows them under "Un categorized". Is there any way to stop this? I want those posts under the categories I have in metabox title (list of categories for meta tag, if I select some category, from metabox title, it should come under the selected categories from metabox title). But it saves the posts under "Un categorized"
All posts have to be associated with at least one category. It might be possible to bypass this requirement but probably doesn't worth the effort.
If you really need to be able to have content without categories then you should create and use a custom post type, with which you can create and use custom taxonomies. It is hard to understand from the question what are you doing with the meta values but it sounds like you are trying to recreate the functionality of custom taxonomies.