I don't know how you would do it natively within SyncToy, but I figured out a round about way to do it. Create a folder pair for the subfolder and another one for the parent folder. From my limited testing (~3 trials), SyncToy runs the folder pairs in the order they are listed, so, if this holds up, you can put the subfolder pair above the parent folder pair, then do a run all. If SyncToy does not always run the folder pairs in the order they are listed, you have two options: run each pair individually from the command line with a script, or create a separate task for each pair (instructions for both are in the F1 help under "SyncToy How To Topics"). If you go the task or script route, you'll have to make sure the first pair finishes running before the second starts; otherwise the second one won't run.
Out of curiosity, why do you have to run the subfolder before the parent folder?