Generally adjustments are made at the needle valve. You can tweak the regulator as well, but any adjustments at the regulator will be extremely coarse so all fine-tuning is done with the needle valve.
The bubble counter is just there to show you the flow rate and has no ability to adjust flow.
Most setups will contain all three components. If you are confident you can skip the bubble counter, but then you need to guess at the CO2 flow rate by the density of mist coming from the diffuser or drop checker color. This will require experience and be error prone.
It will take a bit of play in my experience to get just what you want and it is not likely to stay the same forever. The regulator can only adjust the pressure going to the needle valve. The needle valve is just an adjustable hole to pass the gas.
Most of us are more familiar with using a hose and nozzle so lets think of it that way. Turn the faucet on high and the nozzle down low and you can get "X" amount of gallons through or you can turn the faucet low and open the nozzle and get the same amount? So then you may find you are using something like a reactor that needs very low pressure and you set the reg for that. But if you change and use a ceramic diffuser that won't pass any gas without higher pressure, you will need to change the reg. So how you operate is often a matter of playing both up and down and watching the bubble count change.
A year from now, you are likely to find the amount of CO2 changed when you have more plants to use it. This all gets down to why a good needle valve is so important. You have to fiddle with things and it gets really ugly if the needle valve slips and changes the flow so that you are fighting the adjustments too often.