There are different types of effects which dictate different recording approaches. Here are some suggestions for manipulating your effects to get the most out of them.
A. Some effects, such as ambiences and those effects used to fill out a sound or spread it in the stereo/surround field, are best left to the mix stage. If the performer needs to interact with them, a scratch version can be sent the headphones. Of course, you'll need a separate effects processor for that item in the mix stage or you’ll need to pre-process the track and lay the processing to a separate track.
B. Some effects, such as longer delays (anything longer than a slapback), often need to be played interactively. The performer may either need to play against them in order to create a particular sound or feeling, or may need to make his playing more "lean" to give space for the effect to be heard. In order to make these work, you'll probably need to record them at the time of the performance. If you record the sound and effect as a single unit, you won't be able to change them later. On the other hand, if you have a limited number of effects devices, this method will free-up one during the mix.
C. Here's a third option: If you are recording an interactive effect and you've got the open tracks, you might want to record the instrument and effect at the same time but on different tracks, in order to have the flexibility to manipulate them separately or replace the effect at mix time. The earliest example of this which I can recall is Joe Walsh's The Bomber/Closet Queen/Bolero/Cast Your Fate to the Wind from the James Gang Rides Again album. On the spacey slide solo just before the Bolero, Joe’s pioneering producer/engineer, Bill Szymczyk, recorded the guitar and Echoplex on separate tracks and manually panned the two channels around during the solo in the mix stage. The reissue CD of Rides Again from 2000, where they brought back Szymczyk to remaster the album, really brings the track back to life.