What happens to java in mac osx 10.9.5

I'm working on a Macbook pro 2,5 Ghz, OS X 10.9.5
Im trying to run a program that works on java, the problem is that since its last actualisation the program doesn't open and shows the message: "Unable to run Java Runtime Environment".
I tried installing and actualising Java to its latest version on Mac (arguably this one: Version 8 Update 40). When I did so, the package didn't get installed and it showed the message: "trying to install Java 1.8.40.27, however 14.9.0 is already installed".
In the troubleshooting discussion of the software page i'm using (Zettlekasten, see: http://translate.google.de/translate?hl=de&sl=de&tl=en&u=http%3A%2F%2Fzettelkast en.danielluedecke.de%2Fwiki%2Fdoku.php?i…), programers suggest modifying the operative version of java from the Java Control Panel. The problem is that i cannot have access to such panel because i cannot find java in my computer. It is supposed to be in the utility folder located in the Applications folder, but it's not there.
My questions, how can i make Java Runtime Environment run in my mac?
How can i access to Java configuration in my computer if there is no java control panel or similar?
I'd be deeply grateful if somebody could help me... in the meantime i just complain on mac's unilateral decision of considering that there are, from their perspective, some useless plug-ins as they did with Java...

Hmm. I didn't have that problem - maybe the order you install them in matters.
I have Oracle java 8u40 and:
Java for OS X 2014-001
both installed - they coexist because they install in different locations.
A visit to the oracle java web site shows I have 8u40, and in the Terminal I get:
java -version
java version "1.6.0_65"
(so that's JRE6)

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