Be sure that a 32 bit JVM will run the application using 32 bit constraints and a 64 bit JVM will run the same application using 64 bit constraints. This is handled automatically and it means that a java application is not tied to the platform over which it is compiled. Hence, it does not make any difference to have a Java application developed and compiled over 32-bit or 64-bit machines. It should be machine-independent; unless you have some native library dependency or the java code is directly being compiled to native code.
There will not be any potential compatibility issues and you DO NOT require any tools (which dont exist by the way) to keep your application safe from such issues. The java platform takes care of the same itself.