PHP and Search Engines

I am working with a colleague who has spent a large amount of time working on a large and complex web site. We are looking at using PHP to generate many of the pages. We have set up the server to parse all html pages so you dont see'.php' anywhere. Would search engines have any problems whatsoever about indexing our site? Also I understand that search engines dont always follow links with question marks in them. My colleague is unsure about making a change this big that may result in problems with search engines which we cannot afford. I have asked a similar question before but my colleague is unsure before allowing me to do this. If anyone has anything that they are sure of that they can show me such as a link that talks about this or your own experience - I would really appreciate it. Thanks, Abe