I know what you're talking about. I like to err on the side of slim/slight/caution.
I showed one of my crew how to use the lighting software and the idiot went right to the strobes and kept strobes going damn near the whole time. I was yelling at him "KNOCK OFF THE STROBES" but he wouldn't listen. If I didn't have to ride the faders like a maniac at the sound console, I'd have yanked the DMX cable out and just let the room run dark and let the guy in the projection booth just use the spot.
Sound should be used to bring out and enhance the performance. Likewise, lighting SHOULD be complimentary and augment the performance, not DISTRACT from it. Yes, lighting can be easier to cause distractions with, and sometimes lighting can be a distraction. However, if the distraction is done for artistic purposes, then it's fine.
OK, let's pull this back on topic. How to trigger a strobe within a scene? Well, there are a few ways of doing it. Neither are all that great and some will work better than others.
1: Are you using a dedicated strobe fixture? It really makes a difference. Use the channels assigned to it and drag them up/down as necessary.
2: use a MIDI controller and bring channels up and down. It may be easier for you to do it this way. It is for me.
3: Another option works good with wash scenes. You can make a second scene. For example, make a blue wash scene. Then copy this and add the strobe to it. My suggestion is to have the strobe run for a certain amount of time and intensity and then have it exit back to the simple blue wash scene when done. This option aso works good with fixtures that wash and strobe. This is how I do it.
Other than that, I see you needing to make lots of scenes. Organize and label properly.
Remember, MyDMX is more designed to be a beginner package. it packs a lot, but it can't do it all.