Theming manually is fairly simple, but when you update either the app or the tweak, you'll have to manually replace the icon file again. You can access your application or tweak's icon image by navigating to root:var/stash/applications.xxxxx (a lot easier than root:var/mobile/applications/ then using trial and error to find which folder is which app since they're just a bunch of letters and number in this directory). Find the app/tweak you're looking to theme, then replace the main image with the image you're looking to have with the same name. The image is usually <app.name>@2x.png though it may be slightly different for some tweaks such as iFile's image.
If you have access to a theme's raw files, you can navigate through them, copy all the images for an app, then pasting them onto your device using SSH or iFile to replace the original ones and play around with that.
After replacing the icons, open up MobileTerminal and run the command "uicache", then exit MT and your icons should change after switching from one page of apps to another then back. If not, then respring or check that the dimensions in pixels are the same as the original. You'll want to add a .bak to the original icons just in case so you'll he the originals for whatever reason
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