You can drop it right in for the most part. As long as the engine you're buying has all the necessary parts/accessories. The gearing on the 5s tranny is higher...think of it like a bicycle with speeds: the bigger gears will get you moving more easily with less effort (power). The 5s needs this because it has so little power. The 3sgte has enough power that it doesn't need such high gearing. Using the 5s tranny with the turbo will affect your cruising rpms and will limit your ability to use the turbos power band effectively...but it will work.
Also...if you're using the 5s tranny you can use the drivetrain (axles, hubs, etc) that are on the car. That'll make it easier...just make sure you don't push it too hard...I'm not sure how well the NA axles and such will hold up to the turbo's power.
Here...read this...
MK2 NA > Turbo Write-Up