I have terrible but defined habits for my ROMs. I use the same folder structure for all of them.
./[platform]/[game]/[game].zip
./[platform]/[game]/[game].iso
./[platform]/[game]/saves/...
If it's a series, using Pokémon as an example, I also have:
./Pokemon/Backups/[game].zip
./Pokemon/[generation]/[game]/[game].iso
So it's not that good of a backup, mainly there in case the iso corrupts, but I think it's better than nothing.
A really good way to do linux is to play around and break things, but to have a backup you can restore from.
I don't know about other distros specifically, but Mint comes shipped with Timeshift, which is easily configurable and can be set up to include your home directory. Make a backup on an external drive every now and again so that if you break everything, you only lose a bit of work instead of all of it.
Search engines are your friend. If you want to do something, look it up first (ex/ "How do I [x] on linux") and read some of the answers. Don't just go with the first option you see, and if it looks decent but you don't understand it try looking up the commands it uses to find some documentation.
Learning linux isn't something you can do as passively as you can with Windows, so take time to really try and learn things you're looking to do.
And a good rule of thumb is that if you think your system should be able to do something, it probably can.