I noticed, there are Java 4 different Keytool.exe(and jarsigner.exe) on my computer. For either Java 64bit or 32bit and either in the jdk and jre directory.
Does it make any difference, which one I use to sign my jars?
No, the functionality is the same. It's just included in the jre and the jdk, and if you happen to have several of them, you'll have several keytool.exes.