Hello and Welcome to the community!
I’d like to move from proprietary note taking systems such as OneNote to Evernote to a more universal one, and Markdown files may be the best solution.
Obsidian is the right choice, then. I was after the same things. Future proofed, secure and offline.
How do you handle such files on Obsidian?
Do you embed these files inside the note?
Do you keep these files separate, and simply refer to them in the note?
You can embed certain file formats. Others get stored as an attachment in a folder that you can specify in settings. All in all, it handles it well and I have had no issues in the regard.
Any tip or feedback is welcome.
The help vault usually has a ton of tips and answer to most of the questions one might have at first. If you need help you with any doubt, you can ask the community here or on discord.
I highly recommend this playlist by Nick Milo to get started.
You can check out his Starter Kit pinned to the Knowledge Management Section of this forum as well if you want to dive in deeper. I can not recommend it enough. Though I would suggest you try it after you use Obsidian for a while first.
BTW: I’m looking for a system suitable on mobile too, since I’m always on the road with iPhone and iPad.
You can sync the md files of your vault via any cloud service. You can use any markdown text editor apps like iAWriter on your phone to access and edit your notes.