95 Integra Question Antenna motor and leak in trunk

can someone please help me with a question I have about my 95 integra.
First off, when it rains i get water in my trunk down by spare tire. does not leak when parked, but i can hear it splashing up on drivers side when i'm driving and roads are really wet.
(F.Y.I. after i bought my car used at Carmichael Honda in Sacramento CA, I took to an auto body shop because of this leak and was told by 2 different auto bodys that my car had been in a major accident and basically put back together as fast as possible to sell.)
Anyway, my power antenna was bent so i bought a new one, well i could not get my old one out and the mast was broken in the motor so i ended up having to take out the motor as well to get the antenna out. in order to get to the motor i had to remove the housing in the trunk then the motor was behind some metal frame of the car. it is hard to get a good look in there but i think that this is where my leak is becasue it was wet and all rusted. once i removed the motor i felt back there on the frame of the car and found a hole that is not sealed at all and a piece of inner rusted frame actually chipped off.
the hole appears to be filled with dirt or something, but the antenna motor has a clear tube with a round black rubber plug thing on the end of it which has a hole for draining.
my question is, is this black plug thing supposed to be in that hole? im thinking possible its a drain for water that maybe gets in through the antenna and that this tube and hole are my leak?
sorry so long but any help greatly appreciated