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You already have it running side by side. The only trouble is that the software needs to be built such that you can force it to use a specific installation of Java. It seems to want to use the 'default' one. Only way to find out is to check the documentation of said software or to contact customer service.
I have a similar situation. I have a server equipped with an early Dell Remote Access Card (DRAC). The console-view function requires Java 1.6, and it won't operate if 1.7 is installed. I have found a workaround that may work for you as well: Open the Java applet in Control Panel, then click on the Java tab, then View. You will see your installed Java versions. If I uncheck 1.7 but leave 1.6 checked, I can view my DRAC console. When done I reenable 1.7.
Note that since I installed 1.7u6, there is a new warning message (see thread, "Goofy error message, jre7u6"). This does not prevent me from viewing my DRAC console; it's just annoying.