Question: I'd like to know if I can develop my program with the current JRE 7u45 and later run it on an AS400 with IBM J9 VM build 2.4, JRE 1.6.0.
Or will I have to use the 1.6.0 JRE to develop my program? As long as I don't use commands that were introduced later the program should work, shouldn't it?

Answer: 
If you are careful enough with the APIs, you can make the Java 7 compiler produce Java 6-compliant bytecode, but it is not the default behavior.

I must add that this doesn't seem like a wise way to move; the APIs change in subtle as well as prominent ways and setting the "compliance level" parameters on the Java compiler will not prevent you from calling any methods which do not exist in JDK 6.
While you compile the program you need to use the "-target" flag and set it to 1.6