If the park hoppers do not have the magnetic strip on the back of them, you will have to exchange the ticket for one that does just to gain admission to the parks. You can do this at Guest Relations. The new pass will have a magnetic strip that is read at the turnstile and at all FP machines.
If your PH has the magnetic strip already on the back, you're good to go already. FP was in use long before the MYW passes were introduced.