Automation is a feature in a program that lets you control various parameters of that program. In Fruityloops's case you can for example use it to slowly sweep up a filter, pan a channel from left to right or fade up or down a volume knob on the mixer.
"Main Automation" is a feature dating back from version 2.x which is now thankfully obsolete since version 3 when pattern based automation became the prefered way of doing automation.
It's still there to provide some degree of backward compatability, but automation channels in version 5 really address the problem properly, bringing at least that side of the sequencer up to scratch with it's bigger buddies (FIIIINALY too!)...