1) In order of difficulty (easiest to hardest): Turn based battles, real-time that pauses for turns (ATB Wait style), true real-time (ATB Active style), true real-time that allows characters to move freely (Secret of Mana).
2) These two links explain files needed:
http://www.verge-rpg.com/docs/view.php?libid=3§ion=146
http://www.verge-rpg.com/docs/view.php?libid=3§ion=147
#includes aren't necessary, and *are* only for organization. But it is considered good practice to use them to split up different types code and also to keep system.vc from extending into 20,000 lines or so. If you organize with #includes, finding an error on line
n will be that much more useful.