What is this noise?

Got a 2005 Dodge Stratus 2.7L. The check
engine light has been on for about a year
now with knock sensor reading. About a
month ago, the coolant air bleeder popped
off while I was driving on the highway, I
pulled over immideatly becuase I saw
smoke. After the car was towed home, I
replaced the unit myself and afterwards
added oil as I noticed it was low. When I
started the car back up, I heard a
thuddering, knocking type noise coming
from the lower side of the engine. Since
then I have driven the car seven or eight
times with no problem. I notice the noise
when the car starts, when i accelerate, and
if i have been driving it for more than a half
hour. The car also stalls a lot when I
reverse, especially when i have been
driving it for a while. Keep in mind i am not
a good mechanic at all, so I may have
messed up when replacing the air bleeder
(i follwed a youtube video). What could this
noise be?