We would not recommend merging Javascript and CSS files. See why here: http://fishpig.co.uk/blog/why-you-shouldnt-merge-javascript-in-magento.html
If you wish to merge your all css (or javascript) files in Magento you can do that in your Magento Admin Panel:
- Log in your Magento admin panel then go to System > Configuration.
- From the Current Configuration Scope: Select your Store view then click on Developer tab.
- Now click on Css Settings (or Javascript Settings) Tab.
- From the Merge CSS Files Select yes to merge your css. Default No is selected.
- Now clear your browser cache and also refresh your Magento cache. Your all css files are merged now.