How to assign different ReFit icons for multiple Mac partitions?
I, too, am dual booting 2 OS X's (Mountain Lion and Yosemite). This is because Yosemite is too heavy, so it's there only as a safety net! 

If you are double booting Yosemite or El Capitan with another prior OS X, copy the rEFInd folder to this older OS X. This is because of the scheme Yosemite and El Capitan use to boot, and having the rEFInd files inside these partitions will require special installation instructions. In my case as I said, I have Mountain Lion and Yosemite, so the rEFInd folder is at the root of the Mountain Lion partition (volume).

But in the other hand if you are booting Yosemite and El Capitan (without an older OS X version as 3rd boot) then you'll have to go to the rEFInd page and read how to install rEFInd in these OSs.

This is how it's done:


Download the latest rEFInd from http://www.rodsbooks.com/refind/
The latest version (0.9.2) supports .png for icons, so no need to create .icns files.
Configure your icons and place them in the icons older. I have made a God fearing simplistic theme. If you use it may I suggest you keep the background as a reminder of to whom one day you will answer to! Download this theme (and the binaries). It's basically my rEFInd folder zipped.
Configure the refind.conf file to use manual boot stanzas. These are  hardcoded (in the config file, much like a grub file in linux) options so the name of the volume of your OS X cannot be changed without changing the configuration file. If you fail at this and change the volume name without updating the .conf file, that particular boot option will not be bootable anymore. But since you'll have two OS X's you can force Apple's bootmenu with Alt at the startup, boot the other volume and fix the .conf file. The proper basic necessary configuration is as follows:

scanfor external,optical,hdbios,biosexternal,manual

menuentry "Mountain Lion" {
    icon \rEFInd\icons\ml.png
    volume "Mountain Lion"
    loader \System\Library\CoreServices\boot.efi
    graphics on
}


menuentry "Yosemite" {
    icon \rEFInd\icons\yoyo.png
    volume "Yosemite"
    loader \System\Library\CoreServices\boot.efi
    graphics on
}



Explanation: In the scanfor line you'll have to remove the "internal" option so rEFInd will not scan for the partition (as they are defined with menuentry) or you will have 4 boot options, the two from the scan itself, and two from the hardcoded menuentry sections. Also still in scanfor you have to put the manual option so rEFInd will read the menuentry sections. 
And the menu entry can be explained with this example:

menuentry "Name that Will Appear In The Boot Menu" {
    icon \path\to\the\icon.png
    volume "THIS IS THE EXACT NAME OF THE MAC VOLUME"
    loader \System\Library\CoreServices\boot.efi
    graphics on
}


Leave the "loader" option as it is. Because that is the default path for OX S' boot.efi (on all recent versions).

And finally the graphics on is to hide the rEFInd command like black screen when booting, so you get a nice graphical transition between the boot menu and the screen with the apple (Apple's boot screen).

I thinks this should cover. The end result should be (the rEFInd.zip at the top has this theme already) something like the following




Finally set the boot to be done using the non-yosemite/ElCapitan partition (or the partition where you copied the rEFInd folder to. To do this go to:  System Preferences > Startup Disk click the partition and press restart.


If things go horribly wrong and for some reason you cannot boot, try either Alt to choose a bootable partition (ie. Recovery)



Just a final note, App Store uses Spotlight indexes to identify apps, so before you launch App Store to update apps that are present on both OS Xs, be sure to unmount the Volume with the OS X that is not running so the AppS tore app can find the right one to update.