(it's always a good idea to be more concise on what you're working on, tell, or better yet show us what kind of guitar it is, whether or not your guitar is already routed for a floyd or if you're doing a retrofit,
just telling us you're installing a floyd rose doesn't really let us know how we can help) :icon_thumright:
but from my understanding you'll want to insert the length of the larger part of the stud into the body, leaving the smaller end out of the body, this is where the bridge touches and pivots from, the bridge should be as level as possible when on the studs.
now i'm just restating already present information here.and i don't own a floyd rose equipped guitar, but i have set them up before, however i've never installed one, so i hope someone else will chime in here.
but at a glance, it seems like they need to be out of the body just enough to allow for the movement of the bridge in the range of what the springs will stretch to, and depending on whether it's recessed or flat mount will change which directions it can move.
so any more info you have on what your build is routed for will help alot.
best regards