I have already created few links on a page menu bar. Can i arrange them as i like or the option is only: chronologically or alphabetically?

If you want wordpress/atahualpa to automatically add new pages to the menubar, then yes those are your options. You could roll your own menu and order it anyway you want. Just code the HTML and put it in the header config area in place of the %pages

Another option is the My Page Order plugin.