RE: Y and 2 bats.
The above is not only correct, but in the proper order of preferred methods of doing the set up. The least favorable way to set it up is with the 2 batteries on a 'Y' harness, as this prevents the use of individual/separate switches and charging jacks. Here's a link that gives some very good information, especially the section entitled "Parallel Operation = Reliability and Flight Time" as shown on the left side of the site. You will see that parallel charging is not recommended.