Sure, you can incorporate a fogger into MyDMX. You might want to make a profile for it if one doesn't already exist.
What model is it?
I have the FogStorm 700 with the wireless remote. Works great, ON/OFF, and it also has a maximum ON cycle before it has to cool down and cycle itself. Best I could do is I think there is a DMX adaptor for the remote port, which I am inclined to check into rather seriously.
But, I don't get the issue yet. Do you want a slower output of fog? Some machines, or at least most machines I am aware of, have fog in two levels: OFF and ON(either you're getting zilch or you're getting the fixed output rate until the machine stops it or you stop it before that duty cycle ends).
If you want to add fog as needed, you could give smaller puffs over a longer period of time, which isn't perfect, but may work. You could incorporate a fan to thin it and spread it faster, which again, may or may not do it for you.
DMX doesn't necessarily mean you have control over the "output amount", but merely the on/off.
You can definately do this. You may want to have a controller such as the Korg nanoKONTROL, where you can assign a fader to that DMX channel and then use that to over-ride a scene. In your case, this would be ideal. You can have your scene doing whatever, then pump some fog in and then lower that fader again.
You're saying that FOG and SCENES are not directly tied together. You want to run your scenes as you see fit, and then add fog on an as-needed basis. Hey, if so, that does make sense.
I was working a show last year where the guys had a highly integrated light show and their fog triggers were necessary, not only for effect, but seeing the beams was also part of the show. At times, there was a tiny bit too much fog, but it still worked with their show.
Share more information. Especially the fog machine and hardware you're using.