Modifications on ISA , J2EE 6.40 platform

Hi

I have installed the ISA R/3 on a J2EE 6.40 platform. And now I want to modify the application. But how??

1.Can I use SAP Developer studio?

2.Do I have to use the ISA Build Tool?

3.When I read the Development Guide I can't find the folders and libaries they refer too. (there is no folder called additional-lib, can' find inqmyxml.jar.....)

Please Help