Procedure
Whenever you plan to run a workflow in the background while continuing other work, it is a good idea to run it with less memory.
It is also good to check the box to run Alteryx Designer at a lower priority (found in your User Settings). This will ensure that the Alteryx Engine runs at a lower priority than all the other applications running on the same machine. By doing so, the Alteryx GUI will remain responsive even when you run a large workflow in the background.
It is also a good idea to have the temporary directory point to a separate physical hard drive from your boot drive. If your temp drive points to C:\temp and you run a workflow that consumes hundreds of GB of temp space (it happens), your system may become unstable.
Additional Information