There are meters for ambient, meters for flash, and there are meters which can do both either separately and/or simultaneously.
Yes you set the power control on the Bee(s), and trigger them. They can be triggered from a PC cord from the flash meter, by slave flash, by pressing the fire button, or by a wireless system.
I suggest you go here
and browse some of the clear manuals that Sekonic has nicely put on-line. The Sekonic L-358 is a good meter that does flash and ambient simultaneously. It displays the proper f-stop, with the percentage of light provided by the flash, along with a bar graph showing the flash, ambient and total exposure with one reading. It can also do things like averaging and differencing multiple flashes.