Hi there,
In your situation I would first go with earlier advice and install a sill pan
before you install the door jambs. Sealing the bottoms of the jambs is
good policy. I use a weather proof glue for that.
As far as order of installation goes, you can either attach a sloped aluminum
threshold to the bottom of your door jambs and basically create your own
prehung door unit or you can install door and jamb first and then cut the
threshold and sill cover between the thresholds.
I prefer the first of these two options because there is less opportunity
for water intrusion.
Either way you would need a door shoe with a vinyl sweep on it to create
the seal on top of threshold.
There are many profiles of thresholds to choose from.
Here is an online catalog that you can check out:
columbiaaluminumproductsllc .com/catalog/
http://www.columbiaaluminumproductsllcRemove the 2 spaces before .com to make link hot.
Pages 40, 47 and 48 are good places to start....You would
use the page 40 style if you are going to install threshold first.
Page 47 and 48 if you are going to install threshold after.
Interior finish floor will determine threshold height required.
Lot's of variables but that should at least get you started...
Good luck with the project!
RC/DG