Can we install two verions of Java JDK in windows?

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 ...