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Ask Someone: 2006 Volkswagen Beetle- Leaking roof?

I have a 2006 VW Beetle with a convertible top. 2 weeks ago I had the top replaced by an upholstery company. Last night we had heavy rainfall and I found 3 inches of standing water in the back passenger side of my car. I called the upholstery company that did the work on my car and they said, “That doesn’t sound like a leaking roof. It sounds like a blocked drain pipe.” Whether or not a drain pipe is at fault I find it highly suspicious that 2 weeks after I take my car to have the top replaced I experience flooding for the first time ever! In a further pursuit to understand what could be happening, I have taken the following steps. 1) I have done some basic google searches and while I’ve found information of SUN-ROOF drain pipes I haven’t found anything on convertible drain pipes or where they might be located or how to clean them. 2) I have also performed a basic water test, pouring water over the car from top to bottom and searching for leaks on the inside of the car. NO LEAKS ARE VISIBLE - THE WATER IS VISIBLY SEEPING UP FROM THE FLOOR. 3) I have also jacked the car to examine the underside and see if any water is visibly draining. There is a small opening on the passenger side that is dripping water, I’m assuming that this is the mouth of the drain pipe? Furthermore, I am absolutely certain that the liquid is WATER as it has no weird smell or discoloration. What is going on with my car? Where is this leak coming from? Can I fix it on my own or do I need to take it to a professional? Can I get the residual water and moisture out of the interior of the car and effectively dry it out myself or do I need to hire a professional? Finally - and perhaps most importantly - IS THIS THE FAULT OF THE UPHOLSTERY COMPANY? DID THEY DAMAGE MY CAR?