I too use Logos, but never thought about doing your approach before where you have 2 apps for (it seems) different things. How do you link back to Logos? Did you ever try out their sermon organizer? (It felt limiting)
Logos creates automatic links when you copy text. You can select the type of link in the panel settings.
I too found the sermon builder fairly limiting and only used it for a short while. I also find their notes system awful and don’t use it either. Logos is my reading researching space, but my notes go elsewhere.
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This.
I recall several years ago when markdown was becoming the thing and I attempted to compose a longish report in whatever markdown editor was the one the smart folks at the time were enthralled with. Then I had to move it into a real Word document for client presentation. I gave up; copied the plain text and pasted it into Word; globally replaced the markdown syntax; and never tried to do production-ready work in markdown again.
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I wish I could use Logos notes. It would be nice to have all those related notes together. However, the Logos notes are too clumsy, slow, and disorganized. I really don’t like the implementation of highlights as part of the note system. The speed of Obsidian makes it super simple.
As @svsmailus mentioned, copying the link from Logos to include is pretty easy. Make sure you’re in the panel you want to link and hit opt-cmd-c.
The slow Logos experience is also why I use Ulysses to write sermons. Never tried their sermon presentation mode as I found it too much of a pain to get everything in and formatted to my liking. Logos becomes a very expensive book reader and search tool.
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I’m SO glad I’m not the only one who feels this way. Document formatting is a huge part of my job and markdown is extremely tedious when you’re manipulating different styles.
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That’s my biggest gripe. Logos is slow slow slow. My second biggest grip is that the mobile version doesn’t work without being tethered to the internet. Without the internet nearly every feature doesn’t work.
me too!
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My vote would be for Obsidian because other than the subject matter (I do not write sermons) My uses are pretty close to yours.
I would write notes for me on projects I was working on, blog posts, ideas for future things I might want to or need to investigate, code snippets etc. I create presentations on the SW I am developing, script videos, plan and organize code and organize my geenral reference material. I do not publish much, the blog posts eventially and in the case of video, the final version, I used to use DEVONThink for all my notes and prep work, moved to Libre Office to create presentations for meetings or Scrivener for long form documents.
I moved to Obsidian for the security after losing data to DT. I was dragged kicking and screaming into using markdown for my notes, I used to use either plain text with tabs or rich text where I added colors to text. What I’ve found after a brief, test every plugin and theme, phase is that I’ve settled into a pretty clean system in Obsidian.
The advantage is that I can think and scatter notes across obsidian, link as necessary and then start pulling them together into my final outputs even if they are just for me.
I am still exploring the Obsidian publish options as that might be a way to handle blogs more easily and I’ve seen some cool presentation things done just in Obsidian so I might be able to get rid of using Libre Office for that eventually.
PS After re-reading some of these posts I thought I’d give my thoughts on Ulysses. Basically I’ve never been able to make it work for me. I think I’ve tried it 3 or 4 times and just can’t seem to ever get it to work the way I think and decided it, like Crafts is not for me.
I no longer use Ulysses since they treated their user base prior to subscription appallingly when they switched to subscription.
How was their treatment appalling?
oh? I remember the switch being smooth and almost invisible. I still subscribe, and at a lower annual rate.
They initially made it subscription with no upgrade for existing paid users and then when protests came gave a very short time to jump on the subscription band wagon at a discounted rate. There was a lot of flack around at the time and the app rating went down drastically under protest from long time users.
I’m glad they survived. It must have been very traumatic for them. And, of course, for you.
For notes I really love Craft because it makes creating styles seamless, easy, and graphically appealing. It’s the perfect balance of a pure writing app with essential styling without the extra heft of Word or Pages.
@anon41602260 and @svsmailus - You guys, come on, Markdown was never intended for what you’re complaining it is not good at! It evolved from the days of plain text email and was aimed at bloggers who write for the web.
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And yet the growing number of markdown apps that claim they can do just that are ubiquitous.
That ain’t Markdown or John Gruber’s fault.
P.S. Don’t believe everything you read. 
I’m sorry – did I step on a sore spot?
Not at all. I’m happy using Markdown in the way it was intended. Aren’t you the one with a painful reaction to Markdown?
I use markdown all the time. I just don’t use it for “production-ready” work, as I said. I don’t know why my opinion and experience disturbs you. Hope that feeling passes soon. 
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I find markdown helpful precisely because I often want to focus on content and not formatting. In Ulysses I can easily turn my nearly-plain text into a PDF or Word Document that translates what I wrote into something that looks good and -as importantly - is consistent.
That said, I write academic papers in Word: it’s too fiddly dealing with citations and the precise formatting I have to use in markdown. Zotero + Word = Dream Team.
Horses for courses.
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