Q: Can I prevent Software Updates from launching by stopping WUA or do I need more?

Hi. According to the following link, Software Updates need WUA in order to download. Since we're having massive problems with newly deployed clients running software updates at the same time as it's running advertised software, we're experiencing quite a variety of strange software failures. Since we're currently not able to utilize wake on lan, I was wondering if I could just turn off windows update while installing software and thus greatly minimize the risk of software patches to be deployed at the same time. 
 
Also, if there's a better way, or simply a way to test if it currently is running a software update let me know. I've not tested for this, but does someone know if the popup that tells you to reboot after software updates has a unique name I perhaps could test for with tasklist ? 
 

    Edit: Seems I'm not allowed to link stuff yet. Anyway the link was meant to be to technet bb680712
Also SMSCliUI.EXE seems to be running when it does software updates. Does it only run during/after software update deployments? 

The CM Client itself won't run Advertisements at the exact same time as software updates when those updates are delivered by CM.  Are you sure those software updates are being delivered via CM?  or is it that you have a 'regular' WSUS settings?  Or is it that you are ignoring all best practices regarding software updates and reboots, and software updates install on, for example, Monday, but do not reboot for days/weeks after updates?
 
If you are using WSUS and not Software Updates in ConfigMgr, then my next question would be "why".

I'm not sure how exactly the software updates are configured, but they're using the configuration manager to install, and the collegue who set it up told it not to restart after the updates, as we haven't implemented a maintenance window. And I'm not sure why, but the client DOES start advertisements despite it being in the process of patching, and does start patching despite advertisements currently running. And this obviously makes stuff fail when two seperate installations are trying to use msiexec at once. 
 
I'm mainly packaging software and taking care of collections and reports though, so I don't know every detail about how different things are set up.