Once the beaker count is full you get the science but extra beakers from the city that filled it are lost, then beakers from subsequent cities are added. I believe the most recently founded city's beakers are added first an then the next most recent etc...
This means that if you only have one city all extra beakers are lost or if you have almost all of science coming from one SSC most of that would be lost if adding an extra 10%. If your beakers are spread out throughout a large empire you can average 3.5 turns/tech though since many fewer will be wasted.
This obviously presumes that you're not delivering caravans/freight. If you deliver some freight then you can part fill up the box or completely fill the box before your city beakers are considered and start getting techs much more regularly but you'll find you would need to check the number of beakers you're able to produce and how many you need for the next advance each turn before delivering freight and recalculate if you decide to deliver them if you want to make the most out of it. If the box is nearly full you may not want to deliver them since the science bonus will be mostly wasted (a city produced beaker is needed to trigger a discovery), and you might want to turn the science rate down to get more cash (if otherwise a lot of SSC beakers will get wasted). If the box is nearly empty you can deliver your various freight and may be able to raise the rate enough to get a discovery next turn.
I don't bother with the micromanagement stuff past checking to see if the beaker box is nearly full when I'm about to deliver. I don't generally want to spend time counting beakers to see if I would be able to fill the box that turn if I turned the science up enough - but then I also haven't landed before 500AD.
Edit: Hmm. a close second.