Website or tools that puts pinyin on top or bottom of the characters automatically
I have never looked for this kind of a tool before - good idea! I just ran a search using  and came across an online tool that will do what you ask:

http://zhongwenzhuanpinyin.51240.com/

If you can read a little bit of Chinese, I would recommend trying this one. It will convert your Chinese characters to pinyin and show tones.

I have read on many Chinese website that there is a way to do all of this with Word but I am not familiar enough with this. You can get the basic idea here:

http://office.wps.cn/wpsword/21508-2013-04-10-16-44-20-302.html

Hopefully someone else will be able to explain how that works in more detail.

Good luck!