Yes, you do have to separate them, and I was initially doing it your way with the airline clipped in, then siphoning bbs from the bottom of the bottle, but I was getting too many egg cases in the shrimp. I now use the airline through the cap method, and my hubby drilled the holes just a bit small so the airline is jammed in. I have seen that you can use silicone or blu-tac - putty would work as well, to block any gaps in the lid. the best thing is that you just undo the airline from the pump, hold the bottle in the other hand and lower the airline so you get those nice juicy red bbs from the bottom of the bottle. then just put the bottle back and hook it up again. I strain my bbs through an old coffee dripolator - the one with the plastic or nylon mesh filter. works great, as then I just dunk that in some clean treated water to wash the bbs out, then feed the little suckers. I figured if coffee filter paper wuld work, why not that? I get the feeding done in about three minutes flat, plus leaving the bottle to sit for 5 minutes or so first to let the egg cases float.
By the way, at Underwater World on the Sunshine Coast, Queensland, Australia, they use bbs to feed sick fish. They have two HUGE setups, but instead of using coke bottles they use 44 gallon plastic drums with downlights above and airstones in the bottom, directing the water to flow in a circular motion. You can imagine how many bbs are in there. It is awesome to see.
Good Luck