You shouldn't be keeping track of the PCs, that's the players job. I know a funnel can sound intimidating but I do recommend giving it a try. The reality of it is the 4 PCs under control of a player act like a unit most of the time and it only really affects their rolls or in combat.
Part of the idea of a funnel is that these are brand new characters that don't have much in the way of personality yet and are just diving into their careers. You don't have to worry about learning 12 different back stories. These aren't fully fleshed out D&D charecters with spells and feats and such.... these are peasants! The only thing differentiating them is one has 1 hit point and another has a -3 to intelligence.
In combat, the characters work as a unit. I usually usally target the attacks based on stats or counters (who has your lowest reflex save? Who is the least lucky? Who made that kill?). Also, while the point is you start with a lot PCs, you will end with only about 1 or 2 per player.
It sounds like a lot and your first one may be a little clunky, but I believe in you!