Alternator output increases with RPMs – on a car this means with engine speed. At idle the output of the alternator may be too low for it to provide for all of the electrical load, and so you'll see a discharge.
To test the alternator you can look at the output as you increase engine speed. You should see the output voltage start to climb along with engine speed. By normal cruise speed you should be seeing about 14.2 V.
One other thing you might want to check is the pulley size on the alternator, if the pulley is larger than the original, it will be driving the alternator at a slower speed than the original one and the alternator will need higher engine speeds to produce full output. At idle the output will be lower than your original alternator and it might be low enough to produce the symptoms you're seeing. Or, the new alternator could have piqued your interest in the behavior of the electrical system and you're seeing things you didn't notice before. People are funny that way…
If you're not seeing long term low output problems – e.g., a low battery, slow cranking speed when you try to start, etc. – then I would say "trust your mechanic."