You'll set both computer up to track only 1 "lap" (or split) since during the actual race, that's all that they should track. When you import the 5K turnaround split after the race, the software will automatically increase the number of "laps" to 2.
If there is any concern about the turnaround point getting triggered by those warming up before the race, then go ahead and set the turnaround computer up to track more than 1 lap (with at few minute gap time set on each split) because the software will not import any 'splits' that occurred before the race actually started (according to the finish line PC) or that occurred after the participant actually finished.