Bottle size doesn't matter if you add your priming sugar to your bottling bucket- it'll be right whether you're using 12oz or 2 litre bottles.
However, to an extent, the size of the bottle will change the time needed to carbonate properly in the bottle. A larger bottle means more total CO2 and beer, but roughly the same headspace in the bottle, so it will need more time to absorb back into the beer properly, but if you're waiting 21+ days before cracking them open (nobody ever opens one early....right?) I doubt there will be a noticeable difference.
If you're going to screw up; do so spectacularly. You'll learn more that way.