In the past I just used a knifes pocket clip and put it in the molle clipped onto it. Though I haven't done that over any long periods of time as that was mostly for things like airsofting (I use to airsoft in the middle of no where at a friends property, when I say no where I mean no where it was legal for us to shoot guns there. So a knife came in handy sometimes.) Though I eventually just started using a spare pistol mag holster.
Though if I had to use just molle, I clip it on the inside of the molle as I said before than run some paracord if possible through the lanyard or keyring loop and have a small carabiner or something of that nature hooked up to it. Than another thing of paracord hooked up to molle next to it so I could just hook it onto that so I don't lose the thing. This is assuming you don't need quick deployment. Hopefully someone else has a nicer solution than this.
Though for a 3 layer SAK, a small pistol mag shealth or something of that nature will get the job done, or find a shealth for SAKs I believe their out there. You can also look up SAK's and clips I know I ran across some ways people rigged them to them on the forums but I don't remember where exactly.