I'm assuming the containers represent two independent flows of tools. Regardless of the use, if you have an order in which you need to enforce execution and block until done tool can't help you out then you can achieve this with a Macro.
It's actually a relatively simple approach. And even if you don't have much experience with Macros would make for a fun first dive into Macros.
In a nutshell, you're going to convert your existing workflow into a Macro and use an outer workflow to pass in true/false values to disable/enable the containers as you need per iteration.
I can't upload workflows from my work computer so I'll write out the approach:
Part I: The .yxmd workflow(AKA what I referenced as the outer workflow)
This will involve only 2 tools.
First, a text Input tool with a table that looks like this:
|Execution Sequence||Container A||Container B|
Second, the Macro you are about to create. The configuration here will involve mapping Container A column to the Control Parameter connected to your container A and the Container B column to the Control Parameter connect to your container B inside the Macro.
Part II: The .yxmc workflow (AKA the Macro) will involve minimal adjustments to your existing workflow.
First, you'll need to add two control parameters. The first Control Parameter will be connected to Container A, the second Control Parameter will be connected to Container B. When connecting the Control Parameter, connect the Q icon to the Lightning Bolt icon on the container.
Second, you will notice two Action Tools have appeared between the Control Parameters and the Containers. The configuration will be the same for both. Click on the Action Tool, expand the Disabled section and click on the words value - value='False'. This will highlight that section. That is all the config you will need to do. Note: Select an action type should reflect the default value "Update Value".
If you run the outer workflow you will see two iterations run (because you have two rows in the text input tool) that has passed the appropriate True/False values into the Macro to disable and enable the relevant containers. You could expand this further if you had three containers or more. However, I'll stop right there for now.