There is no one most effective method. You have to do what suits your strategy and your race.
I personally prefer to separate the groups based on the physical positioning they will use during battle. As a protoss player, I typically keep Zealots, Immortals, and non-blink Stalkers in Ctrl + 1, and Colossi and Sentries in group 2, simply because those units work best when they are far away from the front lines. I might use group 3 for either blink Stalkers because they have to be able to move very independently, or possibly for High Templars or an aerial strike group.
In my opinion the way you hotkey buildings is more important than how you hotkey your army. Having units out of position is definitely really bad, especially for things like Siege Tanks and Colossi, but the ability to instantly spawn more units while barely taking away any time from your battlefield attention is more important. My personal preference is to use Ctrl + 4 for all Warp Gates, Ctrl + 5 for all Nexuses, Ctrl + 6 for proxy Pylon, and Ctrl + 7 and 8 for Robo Facilities/Stargates.
Hitting the hotkey for a unit or building group twice will center the camera on it. That's how you see the pros instantly switching views between their army and their base without clicking on the minimap. The following is my favorite solution for the "Warp Gate" problem where Protoss players have to look away from the battle to produce reinforcements.
Say I'm attacking with a main force and I need to warp in, some reinforcements, I double tap 6 to center the camera on my proxy Pylon, press 4 (or W) to select all Warp Gates and warp in some units in the Pylon's power field, select them and press Shift + 1 to add them to my first group, double tap 4 again, hit 5 and Chrono Boost all the warp gates with all my Nexus. This sounds complicated, but once you get the hang of it you can do it at amazing speed. Most people don't know that you can Chrono Boost warp gates to decrease the Warp-in cooldown time.
If you're playing as Terran or Zerg it's even easier to do this. Simply keep your camera on your army, hit the hotkey for your unit producing building, set the rally point to one of your own units or a location near your army, and build a bunch of units.
Also, when building workers for new expansions, I like to make all Command Centers/Nexuses/Hatcheries build workers at the same time and simply send them over, as the worker production speed can be triple or double that of producing workers only at the new expansion itself, not to mention you can build and waypoint before the expansion is even finished building. That's the advantage of keeping all main buildings in one hotkey.