using a KOMA class could help. They are much more customizable. Further they don’t write out “Chapter” and they provide a very good package for headings and footers. The position of the page number looks also like you wished.
Test this small example:

\documentclass[a4paper,10pt]{scrbook}
\usepackage[automark]{scrpage2}
\pagestyle{scrheadings}
\usepackage[english]{babel}
\usepackage{blindtext}
\begin{document}
\Blinddocument
\end{document}

The documentation will explain more, there’s a whole chapter dedicated to headings.

Stefan

Yes you right, with this book or report document classes, the header from the chapter or mains section will disappear which is what i want. The problem with this is again, it puts the page number for that page at the center. I want the page number to be on the right.

I recommend to use fancyhdr instead of fancyheadings, this is an early version. Since you are writing a thesis consider to use another class than article. The article class is appropriate for smaller documents. You could use report or book instead, there are even some dedicated thesis classes.
book and report provide chapters. chapter starting pages would have another style, numbered but without heading. That may be what you would like to achieve.
Have a look at the fancyhdr documentation for explanation and examples. If you still have questions just write them here.

Stefan

there’s no problem in this code. This complete example is compilable without error and refers to both equations:

\documentclass[a4paper,10pt]{article}
\usepackage{amsmath}
\begin{document}
\begin{align}
a &=b\label{eq1}\\
c &=d\label{eq2}
\end{align}
See \eqref{eq1} and \eqref{eq2}. 
\end{document}

Try this one. Perhaps post a complete example here, like I did, that shows the error. Something else causes this problem, not visible in the piece of code here.

Stefan