Of course you can use multiple versions of Java under Windows. And different applications can use different Java versions. How is your application started? Usually you will have a batch file where there is something like
java ...
This will search the Java executable using the PATH variable. So if Java 5 is first on the PATH, you will have problems running a Java 6 application. You should then modify the batch file to use a certain Java version e.g. by defining a environment variable JAVA6HOME
with the value C:\java\java6
(if Java 6 is installed in this directory) and change the batch file calling
%JAVA6HOME%\bin\java ...