The other side is more difficult. We do use a glue like Tightbond. You want the hole deep enough so extra glue has a place to go but not so deep that it is not pushed too far up the flutes. Our hole is 2mm deeper than the dowel penetration. The link has some good info.
What I found over time was that the assemblers will not use enough glue, too much and it squeezes out so they lean towards less. Everyone's idea of enough is different.
I ended up getting a some Jolly Colla glue guns. They were $3,000 in 2014 and they are still working fine.
http://www.omal.eu/en/products/gluing-system/item/jollycolla.html
They are not cheap but It is capable of putting out a metered amount of glue. I set up a program on the CNC to drill holes in sequence deeper and deeper. We then set the glue gun to fill the first hole, lets call it the deepest. Push the panels together and glue squeezes out, too much. Move on down the line until you find one that is the perfect depth. Push it together then pull it apart. See how the glue spread around the dowel without squeezing out.
We then created a glue setup board. It is a board of know thickness with hundreds of 8mm holes drilled in it to the correct depth. In the morning they set the machine fill one hole on the test board and go. Everyone is happy. Glue doesn't squeeze out and the joint is not starved.
There may be an easier cheaper way to do this but I am happy with this method, it is consistent.
We did use Lamello glue bottles set up for dowels. They were not inexpensive either and only lasted a couple years but they did work.
Here is one, I never bought anything from this place but they came up in the search. There is a collar on the bottle that limits the amount of glue on each push. For $110 it really does a good job.