I struggled with many things when I was learning RPG Maker the first time. The one recurring theme that took the most time to really master was how to make things work sequentially in cinematics the way I wanted. Things like, "have character A do a thing during a cinematic, then have character B do another thing." I found the best way to make it work is to try to centralize the commands in one event as much as possible. If I split the commands up across multiple events, there's a risk that the computer will try to make everything happen all at once instead of waiting for each switch to flip or variable value to change. This does lead to some funny-looking events, like one character holding all the commands for all the characters on the map for the cinematic, or having one "controller" event stashed in the top-left corner of the map handling all of the characters' actions, but it works!
Another thing that I still struggle with is battle sequences. While I understand it mostly now, making events happen in battles can still be a dicey proposition that takes a fair bit of trial-and-error to get right, and gets more dicey the more complex the sequence is.
Variables (and switches) are cool. You can do a lot with them just by telling the engine "if this variable = (something), do this." In Unreal, variables are even more impressive: EVERYTHING is a variable! This leads to a level of control not possible in RM, but it also means there's a lot of complexity associated with it - I'm glad that I have all my experience from RM to help me understand what's going on and how to leverage all this power. I hope you continue to wrap your head around variables, because in the end you will be able to make the engine act like your personal trained monkey!