Is there always going to be manual manipulation of the code?

I am doing functional web testing of a java application where there will be many rounds of regression testing as new components are added and/or the database is refreshed. 



I'm having a hell of a time recording a script through and playing it back cleanly. 



There are some pop ups in the application that TC can't seem to deal with and some other pages that are not popups but TC responds the same way to them as it does to the pop ups.



I have around 300 pages in total to test and most of my team is not of the inclination to be writing/manipulating code.  How do I better work with this tool?