jbl,
There are a couple of schools of though on this. The first is to simply apply the filter factor ... intellegently. That means being aware of your light source (e.g., warmer sunlight at morning/evening or incandescent lighting as well as knowing what effect the filter will have on important areas of your scene, such as green foliage, shadows lit primarily by blue light, etc. One modifies the factor and/or brackets to compensate.
The second method is to simply meter through the filter and use the resulting exposure, thus allowing the meter to apply the filte factor. The problem here is that the meter's spectral response is not exactly like that of the film you are using (with the possible exception of the Zone VI modified meter). This is not a problem except with the strongest filters (red, dark green, maybe dark orange, etc.). With these latter, however, modification may be in order.
The third variable is the film's contrast response to light of different colors. This is most important when using strongly colored filters. The response varies from film to film. Note, just using the manufacturers' filter factor does not compensate for this, nor does metering through the filter.
Both of the above methods assume that you have made your exposure determination beforehand. With the first, you are guessing somewhat where e.g., sky values will end up. The metering method gives you more precision here.
I meter through the filters, but have done testing to determine what extra exposure modifications need to be made for the mismatch in spectral response of meter and film (e.g., + 2/3 stop and N-1 with a #25 filter for tri-x).
If I were you, I'd meter through the filter, give a bit more exposure as a safety factor and then keep careful records for a while, compiling data on the filters and films you use. You may find that one filter needs a bit more exposure, or more development, or both, or whatever. These data you can then compile into a table that you can memorize and/or use in the field.
Best,
Doremus
www.DoremusScudder.com