In my master bedroom I have one GE smart dimmer switch on the wall that will turn on my master bedroom fanlight combo. I have it automated to turn on both bedside lights when it is turned on and turned off which is great because now the bedside lights work in sync with the GE switch. The problem is when I create a scene to turn off the master bedroom fan/light combo and keep just the bedside lights on - the bedside lights that are on a GE plug in smart dimmer turn off because there is an automation for them to turn on and off with the GE wall switch. Is there anyway to set up a scene where the bedside lights stay on when the fan/light combo is asked to turn off. It is kind of annoying to have to hit the scene twice to get it to work right. Thanks!
I’m tired today, so I’m going to let other people give you the details, but the easy way to do this as a general principle is to set up an additional virtual device to act as a proxy for one of the physical devices.
Then you can set up rules or scenes which only involve the proxy rather than the real one. And that allows you to have any combination of situations where sometimes they work together, sometimes they don’t.
A common reason for this is when you want to have porch lights come on automatically when you get home and then automatically turn off 10 minutes later. But you also want to separately be able to turn the porch lights on and not have them go off after 10 minutes. Just have them stay on until you turn them off again.
You could set up a proxy for the porch lights. Have the physical porch light switch follow the proxy. Have the proxy light always turn itself off after 10 minutes, but don’t do that with the physical porch light.
Then have the arriving home routine turn on the proxy light. Now you arrive home, the proxy turns on, the physical light turns on because the proxy turns on, 10 minutes later the proxy turns itself off, then the physical lights turn off because the proxy turns off. So far so good.
But if you just turn the physical lights on with the switch, or with a different automation, they will stay on until you turn them off because you didn’t also turn on the proxy.
There are a lot of other reasons to use a proxy setup, including the one that you’ve described. But that’s the general approach. 
Seems like a detailed answer to me!
I would use webCoRE to setup your rules. Just as @JDRoberts explained, you will have more versatility using a either Virtual Switch or a more complex rule engine such as webCoRE.
Saying all of that, if you have the GE Plus Switch, you could actually use one of the “Button” features which are double tap up or down.
This is how I would do it in webCoRE:
If Dimmer 1 (Wall Dimmer) changes to on
And
Dimmer 2 (Plug In Dimmer) is off
Then with dimmer 2 switch
Turn on
If Scene X executes
Then with Dimmer 1
Turn Off
If Dimmer 2 changes to off
And
Dimmer 1 is on
Then with Dimmer 1
Turn Off
This way, Dimmer 1 controls the on function for Dimmer 2
Dimmer 2 controls the off function for Dimmer 1
Now, the better way to do this, with the ability to keep the lights independent, is the following method:
Purchase a Smart Button or a Replacement GE Switch that’s the Plus model. Xiaomi make a decent little button for $10 US.
Use a custom app called Trend Setter which will create a virtual dimmer that will keep the lights in sync when turning off/on and adjusting levels.
Then use the Button to Toggle the Virtual Dimmer on/off.
Use the Dimmers independently without compromise.