Website Security Checks - Server/PHP

We are looking for someone to help us out with a recent Security issue on a couple of websites that was being picked up by Googles Safe Browsing. Google picked this up and on Chrome and Firefox brought up the malware warning with more information that linked through to the following. [login to view URL] On the other browsers it redirected to [login to view URL] which is from code I found had been inserted into the top of one of the sites [login to view URL] file and the bottom of the other. The code has now been taken out and then we resubmitted to Google and they have taken the warnings away. This obviously is just a temp fix and we need someone to check how the code got inserted either from the code or through wrong permissions etc. We look forward to working with someone that has experience in as a Security Expert with PHP coding and basic Server Management. Knowledge of Googles Safe Browsing practices would also be beneficial. PM me if you need any further details.