That 3-1 rule is one of the best in aviation. Personally I don't use the VNAV feature unless I'm told to cross a fix and I have other fixes before I get to that one, as the FMSs I use wont easily give you the distance to a fix unless it's the next one in the Flight Plan. Doing this stuff in your head keeps you sharp and you wont have to rely on automation for something simple like this.
Everyone does it differently, so I'll share with you what I do, and you can take it for what it is worth.
As has been previously said, take the altitude that you have to loose and multiply that by 3. That is the distance which you'll need to start your decent for exactly a 3 degree decent. As simple as that is, it's not really that simple. There's more.
Speed needs to be taken into account, but only on some decents. If you are descending to an altitude at or above 8000ft MSL, you have to consider your speed. Below 8000ft MSL, it's no so important. Here's why:
It's as simple as 250 below 10. If you are descending to an altitude below 8000, you'll have to slow, and below 8, you will have slowed early enough to make the restriction.
At 250 Knots, you need 1250 FPM to maintain 3 degrees. That # is obtained by multiplying your ground speed by 5. That is your rate of decent.
I take the distance I have to go in the decent and add 20 miles to it. That gives me 10 miles to get set up and stable and another to 10 miles to be at 2000-3000ft above the field 10 miles out. That tends to always work out well if ATC keeps you coming down.
As for the Speed, if you need to descend 30,000ft and you are doing 450knots Ground Speed (GS), then 2250 FPM down at 90 miles from the fix is what is required to make EXACTLY 3 degrees. That means at 90 miles out you go right into a 2500FPM decent and 30,000 feet later you are still at 2500 FPM, but once you get there, you pull up to stop the decent. We all know how rough and impractable that would be, so that is why you add the additional distance, in my case, the 20 miles. So if you have a strong tailwind, coming down at 500 Knots and 2000 FPM will leave you 500 feet short for every minute you descend. After 4 miuntes you are already 2000 feet short. The angle is too shallow. Does that make sense?
Now, as you come below 10K, you'll have to slow. When I go below 10K, I sneak the power back to idle at 13K and arrest the decent if need be to 2000 FPM. That will slow me to 250 at 10K like clockwork. Since I am now doing approx 250 KNots (depending on the winds), I only need 1250 FPM, but I keep the 2000 FPM to 5000ft MSL, then it's 1000 FPM to the FAF. With that decent schedule, I've slowed enough (laterally and vertically) to erase any deficit that I acquired in the decent.
Do the math in your head and just play with it a little bit and it'll all make sense. You can also use the VNAV as a back up to check your mental math.