It all depends on how you wanna make your drops. Do you know your Fantom X better than pro tools?
It usually tends to sound better when you "perform" the drops (mutes, solos, breakdowns, bridges, patterns, etc) on your Drum Machine or Sampler or Keyboard, so when you bring it in to Pro Tools it's already put together.
On the other hand, some people like to visualize their drops rather than perform them. You can do this in "step time" I guess you can call it by just highlighting and deleting, muting, etc. OR... you can always record the automation and use solo and mute buttons where you want the instruments/tracks to come in and out.
When it comes to using midi sync... if you don't have it setup or don't WANT to use it, you can always "tab to transients" and find the beginning of the wav of where it started recording and cut everything else off and trim it so it starts there at the beginning of the session. I usually number my bars so that bar #1 starts a little later. This way everything is on time and you can always add an intro later if you didn't track it out in the first place.