so the questions as in the title, I need to run my server application in Tomcat on a System which is 32 bit Windows XP, I am working and compiling on my 64 bit Windows 7 in Ecli
Java doesn't build 32-bit or 64-bit applications - bytecode is portable across different bit architectures.
The only exception is native libraries that you might be using in your code. If there are any then you will have to manually compile those for the respective platform. Otherwise the java code is totally portable across 32-bit and 64-bit platforms.