I have recently installed clang_complete plugin for VIM. Everything looks fine except in popup menu I get a Pink background color which is uncomfortable.

How do I change this color?
Also is there a way to change some other colors, like manual description, directory colors(in vim) etc?
These colors are defined in your colorscheme.
You can search for a better colorscheme or edit the one you are using now. Here is an example:
If you use a default colorscheme, you can add the lines above to your ~/.vimrc.