I use the 1-Click Maintenance option once a week. I ticked all the items in it except Tracks Eraser. After the scan but before running the fix, I look at the shortcuts Fixer to see what shoertcuts are going to be deleted since it will delete empty folders. I keep a couple of empty folders on my desktop to use when downloading or saving large numbers of files so the files won't clutter up my desktop. To keep Glary from deleting the the folders, I just untick them, then I run the fix.
The reason I don't run Track Eraser under 1-Click is I find it handy for History to prefill in the name of a website that I don't keep a link for in my Favorites Bar. I don't visit them enough to warrant a link. I also don't want all of my cookies erased (I block most of them in IE but some are desireable). You may prefer to clear them out regularly.
Also under Tracks Eraser is a link called Options. Clicking it allows you to choose to select tracks you do want to erase or to see more options. One is the cookie manager. Both allow you to choose which you want to keep before deleting the rest (it used to be more difficult to use so I rarely bothered with it but I just discovered they have simplified it).
I'm still learning how to use it myself since I tend to be cautious about what I do with my computer for fear of bricking it (sadly, I'm also non-Geek). I do experiment from time to time, however.