I downloaded JDK for Mac OS X 10.9.1 from Oracle, but I had to install another Java from Apple site once more, as I couldn't launch eclipse with it.
These are two pages that I referred.
Now I have three java binaries installed in my computer.
/System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/java
java version "1.7.0_51"
Java(TM) SE Runtime Environment (build 1.7.0_51-b13)
Java HotSpot(TM) 64-Bit Server VM (build 24.51-b03, mixed mode)
/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/bin/java
java version "1.6.0_65"
Java(TM) SE Runtime Environment (build 1.6.0_65-b14-462-11M4609)
Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-462, mixed mode)
/Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home/bin/java
java version "1.7.0_51"
Java(TM) SE Runtime Environment (build 1.7.0_51-b13)
Java HotSpot(TM) 64-Bit Server VM (build 24.51-b03, mixed mode)
I found that I can easily remove Installation C, however I'm not sure if this is OK.
When I invoked java from command line, it points to Installation A.
java -version
java version "1.7.0_51"
ls -alF `which java`
lrwxr-xr-x 1 root wheel 74 Jan 15 09:12 /usr/bin/java@ -> /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/java
After some setup and test, I have only one Java (1.6) installed. I have Installation B, and now Installation C is linked to Installation A.
For using eclipse, I had to make Compiler Compliance level to 1.6 to use it (from the help java.lang.UnsupportedClassVersionError Unsupported major.minor version 51.0).
This seems to what happened.
Installation of Apple Java
Installation of Oracle Java
/System/Library/Frameworks/JavaVM.framework/Versions/A
I tried to install Oracle Java only by removing Apple Java, but I got installation error, so I guess Apple Java is needed to install Oracle Java.
It seems like that the oracle JDK can be just removed. For eclipse, I could add Installation A as a default JRE from Java Build Path -> JRE System Library -> Installed JRES -> Add ...