Personally I wouldn't touch a tool like Glary Utilities with a 10 ft barge pole. I do not like such optimisers and so-called registry cleaners for the potential they have to cause damage to the system.
But that said, it's your choice.
There is no simple answer to your question, and you have pointed out some of the ways this is done.
1] Installed software will tell you there is an updated version when you use that software.
2] Installed software sets a service or a process that 'continuously' checks on the internet for updated versions whether you use it or not, and pops-up a message above the Notification Area, (where the clock is).
3] Installed software is passive, and does nothing to tell you if an update is available.
4] When you are notified of an update, there are clear instructions on how to implement the update.
5] When you are notified of an update, and click, the software updates itself automatically.
6] When you are notified of an update, there are no instructions, or the instructions are vague and confusing.
7] Any combination of the above.
What to do? As the end users, we are wholly in the hands of the software developers, and that usually means we have to do some research if we are not sure.
What do the Glary Utilities web site say about updates? Do they have their own forums?
Sometimes we just have to jump in, and run that file.
Windows XP, SP2 using Google Chrome. Most of my software programs send a quick-launch icon to my taskbar, with a pop-up to "install or not" when there's a new update available. When I click on "Install Now" a rectangle immediately appears and shows that my existing program is automatically updated. The new version number is reflected on it's same desktop icon (I checked). A few programs send just a pop-up message without the task-bar icon that, when you click on the "Install Now" option, automatically open your browser and take you to their download site where you can click on "DOWNLOAD" for either their current free or pro versions, but it doesn't have any instruction on how to UPDATE your existing program. My Glary Utilities today presented a pop-up saying there is a newer version available, and I clicked on it's "OK TO INSTALL NOW" option. It automatically opened my Google Chrome browser and took me to it's official download location at CNET.com (great - It's been checked for malware!) but there's no place to click on UPDATE; only DOWNLOAD free version or pro version of Glary Utilities! There is no explanation of what to do for an update! What, am I supposed to uninstall Glary Utilities I already have first? If so, it should instruct to do that! What's the proper way, please?