Car alarm help!

[Integra10]

I recently installed a new deck and now my alarm is screwed up. The keyless entry still works but my alarm won't arm properly. Every time you open the trunk the alarm goes off but the alarm doesn't work for the doors (meaning if you open door alarm won't sound.) Could it be from when I disconnected my battery everything reset? Is there any way to arm it properly myself? The alarm is an alpine sec-9428. Any help would be appreciated. Thanks!

[Strugari]

Do the interior lights light up when the doors are opened? If so, check the connection to the door switches. If the lights do not, then you will need to check your door pin switches.