For a all tubes system with more then a single output (jar usually) you need manage the possible options with valves, i.e. you close valves until there is only one possible route for the essentia to flow, or you get "pressure leaks" and the system doesn't work right.
It shouldn't be a problem in a task-oriented automated system like a setup to produce herba for lamps of growth or ignus for the Infernal furnace, etc. It IS a big problem for many people (like me) who built a single alchemical furnace and walls and walls of jars linked by tubes to power their infusion altars (too many possible outputs now). However for most designs you can replace the tubes with an alchemy golem, which is now easier to get due to the new research system, the only time that won't work is if the jars were suspended on a ceiling as was pictured earlier in the thread. Or some other setup where the golem simply can't reach the jars.
Otherwise you have to put valves on top of each of those jars, and open/close them manually or with redstone signals. Which is a pain. It is really the only negative I've noticed to the new update, and it's motivated mainly by performance reasons (the other way was lag causing issues when the tubing system got above a certain size).
Edit: Also you can still fill jars manually, it's actually slightly easier and faster now, just click the Alembic with an empty jar and you take all the essentia in one go.
Edit the Second: Also this is all based on observation and listening to others discuss it, I'm pretty sure it's not well understood yet, and it's possible some mutli-output tube setups may be possible without a valve on every single one, but at the moment that's what people have played with it so far have resorted to, or they just switched to using a golem (like Dire did).
