Like the others have said, this is absolutely possible. I actually do this myself to get co2 into my three tanks, although I don't use bubble counters (anymore) and rely on drop checkers and observing my fish to tune the co2.
My set up is a 20lb tank>Matheson 3122A-N/I dual stage regulator>a single Burkert solenoid 00463938 with 008409 plug connection to a timer> then three Fabco NV-55-18 needle valves, one for each aquarium. I got the regulator as new-old stock on evilbay for a great deal after trying to modify my co2art regulator to have the output be split; I've never seen threads get damaged while unscrewing something from them, but I swear that's what happened to the aluminum body when I tried to take the original fitting off.
My diffusion methods are a cerges reactor and two standard diffusers, one fluval brand and the other is a do aqua. I did have trouble with trying to run an atomizer diffuser I bought from Aqua Forest Aquarium, although I don't think that was so much a fault with my set up as it started to bubble out of the seam of the cap. That being said, it's easier to tune the co2 when all the injections methods you are using are relatively similar in operating pressure, so I'd recommend either all high or low pressure methods. I'd also recommend setting up the co2 for any new tank on a weekend that you'll be home so that you can check your tanks every couple hours to make sure you don't gas the fish in them. Bubble counters or not.
The reasons I don't run bubble counters are if you get one with a built in check valve it's only a matter of time before that fails, and if you're running them directly after your regulator without a back up checkvalve between them, you're now risking that nice regulator. Even if you do have a backup in between it's not clear when you start relying on it and still run the risk of that failing and ruining your nice regulator. Bubble counters are also a weak link and in my opinion and too much of a hassle to outweigh their perceived benefits. If you're dead set on running a bubble counter I urge you to put it close to your tank, after a check valve and to only put water in it. I've ran mineral oil in one, like some suggest, and accidentally had the pressure too high which blew all the mineral oil into my tank, not horrible, but a pain to clean up. Took two rolls of paper towels to soak up the oil slick. I'll admit that was an operator error on my part. So I recommend you run your setups sans bubble counters and just make sure you have check valves at the end of each line close to your tanks in an easy location to inspect for failure.
Lastly, beware of multiple tank syndrome. I have three tanks, a 17, 10 and 5 gallon, all set up within a year. And I'm going to upgrade the 17 to a 112 within a week. :|