Since an effect you create in ConnectFX is a setup applied directly to one or more timeline segments, you can choose to render your CFX directly in ConnectFX, or wait until you return to the timeline.
To help you organize outputs, you can automatically name an Output node with the name of any output socket in the process tree. With the Output node selected in the schematic, press n and click a node output—the name of the Output node is updated. If you want to change the Output node name, or if you change the name of the original output socket, simple redo the naming process.
You can output alpha results in addition to the RGB result from a CFX Output node. You connect the RGB result to the front input of the CFX Output node, and the alpha result to the matte input of the CFX Output node (The output node now displays CFXa). Both results are fed directly to the timeline.