Do you update using APT or Software Updater and Gnome Software?
Both, really. If I'm fishing for an update to something I installed from a repo, I'll use APT and update everything. I also use APT periodically to do autoremove. Otherwise, I largely use software updater, because it gets the APTs and the flatpaks as well.
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I am using Pop! OS. I always use the terminal.
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I use all 3. Over the Gnome Store are coming Flatpak and Flatpak-related Updates and for the System I use the Terminal and the Software Updater. For me the good Point with the Software Updater is, that You not only see what You are updating. when You click on the Update, You get (mostly) in the second Half the Changelog.
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I usually go for the terminal. Unless I'm on Mint and feeling a bit lazier, in which case I use the mint updater. On KDE I use their GUI software store as well but more rarely. On gnome I only trust it for flatpaks, due to bad experiences I had with it on Z16 with native packages
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Depending on machine limitations, it usually is more efficient to use the Terminal and less chance of freezing, particularly when running an OS with Plasma 5.27. I recently received notification via e-mail from SoftMaker of a new service pack for SoftMaker Office 2024 Professional. I tried to install it via Discover (KDE equivalent of Gnome Software), which also notified me of updates. I'd had several freezes updating my good lady's computer with the single Athlon 64 processor rig with 2 Gb RAM, and 512 Mb AGP 8x Graphics card running Q4OS. After a freeze having used Discover, the nice thing Q4OS is it advises what terminal commands are needed to fix incomplete updates, in the first instance:
sudo dpkg --configure -a
To install updates instead of Discover, I used:
sudo apt-get updates && sudo apt-get upgrade
Then to deal with the broken partial update of SoftMaker Office, I went to SoftMaker Office site and copied the installation comnand of:
sudo apt install -f ./softmaker-office-2024_1218-01_amd64.deb
Strangely, the terminal progress bar of installing the service pack froze at 20%. I looked at the Tower's front L.E.D. panel and the hard drive indicator was spinning so whilst the display on the monitor indicated a freeze, the drive had not frozen. I left it for a few minutes, then pressed the soft reset button. After logging in I checked for updates to SoftMaker Office via the check for updates function and there were none so the service pack did get installed.
Using apt is one of the simplest commands to keep your system clean with:
sudo apt clean
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All of them, to ensure smooth sailing!
If I'm not wrong, Softmaker Office has it own Repo. You could integrate that and then updating it with sudo apt update && sudo apt upgrade