If you've never used Logic for drum replacement before, it's time you learned the basics...
Logic Pro doesn't have an official drum-replacement protocol; its Audio-to-Score function handles this job — providing you know how to use it. Audio-to-Score is one of the Factory menu options visible in the Sample Edit window, and it has a number of adjustable parameters that help with drum replacement. These include Velocity Threshold, for example, which allows Audio-to-Score to discriminate between wanted notes and low levels of spill or noise. Velocity Threshold can be really successful in separating out the various notes or drum hits in a cleanly recorded track, though I find that it often works more reliably if the track being processed has been cleaned up a bit first. We'll come back to the Velocity Threshold setting later; first, we need to do some housekeeping.
When replacing drums, spill from other drums and instruments is often an issue, so pre-processing the track using a low-cut filter (50Hz for kick drums, 150Hz for everything else) to remove subsonic lows, and following up with Logic's Noise Gate, usually yields an improvement. The Noise Gate has side-chain filtering, so when you're replacing a snare you might need to adjust the filters to reduce the lows leaking in from the kick drum and the highs leaking in from the hi-hat. If you concentrate on the 500Hz to 1.5kHz region, the gate will respond well to the snare, but shouldn't let other unwanted sources through. Keep the attack time fast, so you don't lose any transients, and set the release time fast enough that the gate closes fully before the next hit in the track's fastest fill. You're not after a good sound here, just a reliable trigger.
Tom tracks may be processed in a similar way. You can use the low-cut filter to help kill the resonant drone that is caused by the tom heads ringing in sympathy with every other drum and instrument in the room. However, as a typical song contains relatively few tom hits, the Scissors tool and the region Mute buttons can be used to isolate and mute all the sections between tom hits if producing a reliable trigger is becoming problematic. This is often necessary during tom fills, where the close proximity of the upper toms mounted above the kick drum leads to a lot of spill. So, if you don't edit out the unwanted hits, you'll very likely pick up hits from both the toms, rather than just the one you want. The cut-and-mute strategy may be used to clean up any other drum parts that won't play nicely.
The overhead mics pick up a blend of all the drums, so can't be replaced by any standard automated means. If the sound of the drums in the overheads doesn't match the samples you're using to replace the close-miked drum sounds, the best option is to use low-cut EQ to thin out the drum sounds in the overheads. That way it will be mainly stick transients and cymbals that remain. A side-benefit of the EQ is that it will reduce the risk of slight timing errors in the replaced part causing audible low-frequency phase cancellation. Of course, the most rigorous approach would be to bounce the samples as audio files and then compare their waveforms with those on the overhead tracks to ensure that the hits are of the same polarity, and their attacks are in perfect time alignment. Whether you need to do this or not depends on how the end result sounds and how much time you have available. In any event, it may be worth patching in Logic's Gain plug-in (from the Utility Plug-ins), which also has a polarity invert button, to see which gives the best sound when the replacement close-miked drum sample and the original overhead mics are combined.
Having cleaned up the close-miked drum tracks as well as you can, you should now bounce them, using 'Bounce In Place' from the Region menu in the Arrange page, to make the processing permanent. Select all the regions in the track before bouncing. The default option is for the bounced part to be placed on a new track and for the original to be muted. This is useful, as you can always go back to the original if you need to. Finally, normalise this track (via the Sample Editor 'Functions' menu), so that the Audio-to-Score process gets the MIDI velocities in the right ballpark.
The process for replacing each drum part is identical, so I'll just run through the procedure to do it for the snare-drum part:
A further strategy you might employ — in cases where a fast drum fill is giving you problems — is to move just the section containing the fill to a separate track and process it with the Fast Drums setting.
At this stage, you should be ready to hit Process, following which the new part will appear as a MIDI part in your new instrument track. But, before doing anything else, open the Score window for that part and select all the notes, by pressing Command-A. What you're going to do now is change all those randomly pitched notes to the MIDI note needed to trigger the snare-drum sample. You do this by holding down Command and then changing the Pitch value in the inspector to the left of the screen. This causes all the notes to jump to the same value, after which you can scroll through to the note value you need.
Close the Score window and you'll see that your MIDI track now shows a row of identically pitched notes at velocity levels extracted from the original performance. You may want to modify the dynamic response by either adding a fixed value to the MIDI velocities or by using the Dynamics parameter to increase or reduce the dynamic range. You may also wish to adjust the velocities of individual notes where the drummer either played at the wrong volume or where the software may not have got the note values exactly right during complex fills.
With just a bit of housekeeping and a few tricks from the Audio-to-Score function, we've learned how to do some basic drum replacement in Logic!