after i change Merge CSS and JS Files to yes, the add to cart button is not working so the customer can not add products to the cart.
Somtimes you'll find some errors trying to merge Prototype and jQuery librarires. If the problem isn't into your code you can try creating groups.
Into your layout definition, change the addItem action and add the instruction.
All the files with the same group will be merged into a separated file. Some times solve this kind of problems.
First option is to go through all .js files in the /js -> /varien folder and add a semicolon ; at the very end of each file if one doesn't already exits. You may want to do this to your template .js files as well. If you can update this post with any errors you see, we all could help you pinpoint the issue. I would recommend Google PageSpeed if you can't figure out the problem. This webserver mod can minify, compress, and merge js and css files, among other things.