93 audi 90 anti theft

i have an 1993 audi 90 cs quattro. i replaced the batteries in my keyless entry and then tried to use the rmote to unlock the doors. it didnt work but what happened is that now everythin is working backwards. when you unlock the doors it arms the alarm and wont allow you to start the car but if you lock the doors then the alarm is dis-armed. how do i solve this problem? i dont have a button in the car to lock and unlock the doors from inside. any help would be great! thank you