Linux

I'm a regular user of Linux systems but apart from a couple of test Ubuntu installs many years ago they've always been containers or VMs with no DE which I can throw away when I break them. The Steam Deck showcasing how far Wine/Proton has come combined with Windows being Windows has given me the push; I've made a Mint live USB and it's running beautifully on my desktop. I come to you, the masters, with questions before I hit install:

1. What do you recommend I do about disk partitions? I'm keeping a Windows install for the few things that demand it, does Windows still occasionally destroy Linux partitions? Do I need separate partitions for data and OS? Is it straightforward to add additional distros as new partitions or is that asking for trouble?
2. Is disk encryption straightforward? And is that likely to upset the Windows partition?
3. Is cloud storage sync straightforward? It's my off-site backup solution on Android and Windows (using Cryptomator with Dropbox, Google Drive, etc) but I don't think that many providers have Linux clients. Is something like rclone recommended?
4. Should I just use apt to install software? I know there's some kind of graphical package manager (synaptic?), does that use apt under the covers or is it separate? Is it recommended to install something like Flathub too?
5. Any other pearls of wisdom? How do I keep everything tidy? Any warnings about what not to do? Should I use a particular terminal emulator or Firefox fork?