Bobo, it all depends on whether your camera meters through the taking lens... If so, then the meter "sees" the filter and automatically compensates. Othewise, you got an underexposure by 2 or 3 stops depending on what red filter you're using. A light red 090 (Wratten 25) has a 2-stop factor while the dark red 091 (Wratten 29) has a 3-stop factor. The factor actually varies a bit according to the color of the light (less factor in reddish light), and the color sensitivity of the film (some films have less sensitivity to red light than others)
So if you had your separate meter set to 320 for APX400, and you were using a #25 red filter but didn't set a compensation for the filter, you were effectively shooting at EI 1280 (2 stops under). If your meter is TTL, then all is cool and there shouldn't be any underexposure. Make sense? 🙂