I have a 2001 beetle and the key fab for the alarm doesnt work only if you lock the car using the key I changed the batteries in the key fab and IT still doesnt work?

If you rule out the more serious problems, of something wrong with the alarm, or the remote itself is defective, then it sounds like the remote needs to be programmed.
On a 2001 Volkswagen, this is a process that requires two keys.

Insert master key into the ignition lock & switch on the ignition (do not start car).
Using second key lock the vehicle from the outside manually (use key in door lock).
Press unlock button on the remote control one time, wait at least two seconds or more.
Manually open car using key in door lock.
Remove key from ignition.
Test your remote.