Having recently run my first SR5 game I too found keeping track of Initiative to be a difficult task with everything else that was going on. Since then, I've decided to find a better way to go about doing it and the best thing I've found so far seems to be keeping track of it in something like Excel or Open Office. Obviously, you'll need to have a computer in your GM arsenal, but if you do, it doesn't get much simpler. You have one column with every active combatant's name. The second column contains their initiative score. You drag the cursor over the cells in both columns, then you click the little AtoZ button at the top and it'll arrange them in order of Initiative score from highest to lowest. Definitely going to try and work it into our next game.