Hi wejourney,
Sounds like you have the same problem as I had. I found the floor under the front seat was saturated and if the carpet and foam was pulled back I could easily have kept my goldfish in there ! The water was then flowing backwards and filling the storage bins as you described.
The car went into the dealers for 3 days last week and they found the following:
Floor Bungs under front seat loose and allowing water in/out
Sill drain holes blocked. They said it was common if car parked under trees (which I don't actually do)
Cleaned out drains, replaced floor bungs and water tested (through car wash and on wet road test)
I am yet to see if this has worked. We've not had much rain in Wales in the last few days, believe it or not ! It won't be long before the rain returns and gives me a good opportunity to road test myself.
I would advise you insist on a loan car (under warranty) and have the Journey put back into the dealer for as long as it takes to put in right. Have them test it exhaustively before you take in back.
Good luck,
Best Regards,
Jon