The Effex scene's nodes are executed inside of a series of pipeline stages. The stages are chosen to support a certain chain of nodes and group them in a meaningful way for simulation purposes.

The nodes are executed one by one or in chunks. Each node can decide himself how he wants to be executed. The framework also here doesn't care about the input, it just really takes care of executing it.

The user can choose himself via the Pipeline Viewer when the nodes are executed so you are excused to not think about it that much. But the order in which nodes are executed is of course important.
But codewise, there is nothing you need to do. It's all handled automatically.