This is pure speculation but up until 5.0 there was no run.conf.bat. However for Linux there was run.sh and run.conf so someone created run.conf.bat on Windows to align it closer to Linux. And in typical open source fashion, that person didn't think that documentation was necessary (after all, if you want to know how anything work. read the source).
1) Yes, this is the correct way to do this.
2) The service.bat file needs major rewritting to work happily in a multiple service environment. To see what I use, grab the source code for JBoss in Action (http://www.manning.com/jamae/) and look at ch15/src/service/windows/service.bat. This file is set up such that you can set all configuration items at the top of the file (rather than changing the same things all over the place). You do, of course, have to make a copy of the file, one for each service.
In this regard, AS 6 and 5.x work the same.