Watch this video. I think this is what you are talking about
https://youtu.be/dAQi4Uzi8PY
This is a great video of how to fix it. Not the video I found when I had to deal with this a few years ago. Based on the JK Water Leak PDF File, it could be caused by many things such as the foam sticky stuff on the roof, the A or B piller seals, door seal, door alignment, cowl seal, etc.
I was getting a very large puddle under the carpet on the driver and passenger side. Doing this door seal fix worked great for a time. Probable due to buying the wrong weather stripping/door deal material I had to replace it about ever 7-8 months. This is a very common issue with the '08 and '09 model JK's as the B-Piller seals changed they were only used for those two years. Last I heard (a year ago) they had a -8,000+ B-Piller Seals on back order (per the dealership). As it does not always let the water run in on the front part of the door, but back where the corner of the door meets the roof and body behind the seat (the part that latches). It'll sneak in through there too.