You don't need eclipse to be running as 64-bit unless you intend to use well over 1 GB for the IDE. You can use eclipse to develop 64-bit applications by configuring it to use a 64-bit JVM when running your application.
Note: Java switches between 32-bit and 64-bit transparently (not as simple for native libraries but this can be done also) This means that developing for a 64-bit application looks and smells exactly the same as a 32-bit application. All you get is the warm inner feeling knowing that you are using 64-bit machine code and a bit more memory. Note: using CompressedOops reduces the memory overhead at the cost of some CPU overhead.
If you need to use more than a few GB of memory, that is when 64-bit make a difference, but your code will be exactly the same and no re-compile is required.