Hope the wedding is going well!
Here are a few thoughts to mull over.
: 0 OFF, or disabled, that is, the flash will not fire unless it has enough charge for the metered exposure.
:1 ON, enabled, the flash will fire when triggered with whatever power it has in the capacitors, this will often lead to underexposure and is not the default setting.
With regards the auto scan and radio channel selector. Very much leave it on auto, though do make sure you have programmed in a four digit ID number. Auto channel select works very well and the only reason I can think to bypass it is if there were several photographers shooting with complicated setups and you were causing interference on the "best" auto selected channel. In that situation I'd do a manual scan and pick the second or third best channel, if you do the manual scan there are often one or two bad channels.
With regards the ST-E3-RT, I have found it eats batteries, even without an external pack on the flashes the two AA's in the ST-E3-RT will die long before the 600EX-RT batteries do, go figure!
Also, remember that which ever master you turn on first will be your main master. To work smart and give your on camera flash a rest when it isn't used by the 6D, turn the ST-E3-RT on first, then the 60D mounted flash and make sure it is set to master (the Link light should be orange), and then the remote, on the ST-E3-RT turn off Group A, this will prevent the 60D mounted flash firing but will give you the remote fire, on the 60D set that Group A to whatever you want your fill flash to be, normally ETTL. (Of course you can set that up for either to be the main master and fire, or not, the 60D mounted flash, but that suggestion is the logical way my mind works!)
Another thought, although you are using external battery packs there is a choice on how these work. The flash MUST have good batteries in it for actual flash function, the pack only helps the capacitor charge, not the actual running of the flash, one bad battery in a flash can stop it working even if all the other 11 are good.
C.Fn-12 separates external and internal power use, by default (setting :0) the flash will charge from all 12 batteries when an external pack is fitted, but you can ensure operational longevity by separating the external to charge the capacitor and the internals to run the flash (setting :1), this will decrease the recycle time slightly, but should result in more reliable flash operation.
One last observation, when a flash drops out the rest work, therefore, if you get neither flashes with the ST-E3-RT (assuming you have both groups turned on as a test) but do get one or both with the 60D mounted master then you have a faulty ST-E3-RT. I have noticed if I am in ETTL and I lose one flash (normally due to batteries or I didn't reset the wireless button after a battery change) if it didn't fire on the preflash the others will make good the exposure, if it did contribute to the preflash then I get an underexposure, if I am in manual then I just get underexposure, which all makes sense if you think about it.
P.S. Thanks unfocused for that vote of confidence.