I'm doing this soon.
I am going to splice the head unit's wiring harness to pull it off. I will have an aux fuse panel hooked up to the 2nd battery and a 10 amp fused wire running from the aux fuse panel to the stereo harness. I'll then add a on-off-on switch to the power going to the HU. The first "on" will be the line the from the 2nd fuse panel, the other "on" will be the original power line from the stereo harness. The "default" for the switch will be pointing to the 2nd battery, the switch will only be flipped if something kills the 2nd battery and I have to drive for a significant amount of time. This switch will be somewhat hidden as it shouldn't be used regularly. I considered just leaving quick disconnects so I could manually connect the wires.
EDIT: The above may need to use a relay depending on the AMP rating of the on-off-on switch.
Once I get that hooked up, the stereo will be powered from the 2nd battery, but that won't be too useful because the car will have to "on" in order to turn on the stereo so I will also have an on-off-on switch hooked up to the ignition line of the wiring harness. The first "on" will be the original ignition line of the harness so the stereo will function as normal, the other "on" will be constant low amp line coming from the aux fuse panel which will turn the the radio on regardless if the key is in the ignition. The off will obviously turn the radio off.
I will have a build thread that'll document this once I get it all set up. I already have my stereo's ignition line hooked up to a relay and a switch so I can flip the switch and the radio will turn on regardless.