It totally depends on how many attractions you want to do at HS. If you can knock everything out at HS during EMH and the first 1-2 hours the park is open, then I'd do your FP at MK. If you're wanting to do more at HS, then I'd do your FP at HS in the morning and hope for the best for rolling FP in the afternoon.
I'll add in a 3rd option -- schedule only 1 FP at HS and as soon as you tap in, go ahead and schedule your remaining 2 for later in the day at MK. We do this often at Epcot as we really only need 1 FP for that park when we go at rope drop (for either Test Track or Soarin', whichever we don't go to first). This strategy just lets you have a better selection of same day FP at MK since you're selecting them early in the day.