How to update the template quickly and safe way?

hello
Three of my websites have been hacked this week. All of then used a "gavick template".

i recognize that i'm guilty, because i didn`t update joomla to 2.5.14

Malware was "installed" in index.php file of the templates and i`ve cleaned it. Fortunately my sites are online today.

i've seen in gavick's template de Option. "UPDATES", but if i choose the newest, all template files are downloaded, so if i update this files via fpt, i suppose all files on server will be changed.

Can you help me with this questions?

should be templates updated for security?
If my templates files are modified, especially CSS files, can i update my templates?

If You have modified core css files and not used override.css and also modified core template .php files, then upgrade will override them all. The only suggestion that comes to my mind is to download new template and use developers software like diff or merge (winmerge) to see what has been changed and to merge them into new template.
Template updates usually fixes some graphical bugs, adds new features etc. In most cases they are not connected with security.