Standard bosses:
Curly is a standard, entity based boss. You set the entity, and to begin the boss fight you would use a command similar to this:
#0200
<BSL0300<ANP0300:0010:0002<END
#0300
<KEY<CNP0300:0117:0005<ANP0300:0040:0004<WAI0080
<PRI<MSGOh I am slain!<NOD<END
In this example, 200 is the event that starts the fight and 300 is the event # of entity 118, curly-boss. That'll give you a basic boss fight with a health bar. Also, "Run script on death" I think needs to be set as well, in the entity flag list.
Super-bosses:
Each of the eight (nine?) large bosses such as Monster X or Core have a hard-coded location: You can't change where they show up on a map, so you'll have to build the map around them. To start a boss fight with one of them, the command is something like this:
#0200
<BOA0010<BSL0000
#1000
Script for what's to happen when boss dies.
I've never used large bosses before, so my word isn't exactly the most valuable, but that's what I've surmised by looking at the scripts in CE. As far as I can tell, each boss has a special # that you need to know (Monster X, from above, is 0010. Core is 0200) and also, you mustn't forget to put your boss on the map by setting "Boss Fight ID" in the map properties to the appropriate boss. Otherwise, nothing will work (just for large bosses)
My best advice would probably be to try and emulate the original scripts as best as possible, because some entities (like curly above) need to be animated first and whatnot.