2000 eclipse gt remote start

the remote starter is installed and cranks just fine, the issue that i am having has to do with the transponder bypass.  do I have to place the loop antenna inbetween the key cyclinder and the "transponder reader"?  My issue is that the shielding wasn't allowing me to so i had to take it off.  And the r/s was working until i took everything apart to solder the conenctions on the r/s and then it worked again before putting all of the covers on, but once i put the car back together the car would just crank.  So i put the a key in the cyclinder and hit the r/s and it works.  the key was held in palce by velcro in the transpoder bypass so i doubt it shifted because it was a pain to take the key out.  Am i placing the loop antenna wrong?  Has anyone else had any issues with the same year model car?  I am using a valet 561r and a crime stopper bypass unit.