In situation one, I selected 5 fields. I then used 4 of these fields to determine what table to get data from next using PHP.
In situation two, I selected 7 fields. I then used 4 of these fields to determine which of the extra two fields were needed. Since I did not need to make a second query ever, this was faster.
So it would seem, on this smaller scale, that less PHP lines/queries is better than returning MySQL results.
0.00248 seconds
vs
0.001394 seconds
Note: The queries are a lot more complex than listed here with joins and unions so the time is longer than a normal query either way.
Time was measured from before the first query to the end of some printed lines showing the data was selected properly.