Yes. There can be a significant tonal difference between the 5-way rotary and McCarty switching, depending on what you've selected. Be sure to follow Shawn's advice.
The 5-way rotary is designed to access individual coils within the humbucker and use them in different combinations (like singles in parallel or a series). In the case of the old (non-PCB) rotary, you can customize it to achieve lots of different combinations. If you have a newer CE, chances are the 5 positions give you something like this:
Position 10: Humbucking treble (bridge) pickup alone
Position 9: Outside coils of both pickups in parallel for what PRS calls a "deep and clear" sound
Position 8: Series single coils - PRS describes this as a "warm version of the classic in-between the bridge and middle pickups"
Position 7: Parallel single coils - Here PRS describes the sound as a "crisp version of the in-between the treble and middle pickups"
The 3 way gives you the full treble pickup, both pickups (full), or the full bass pickup. IF you add a push/pull tone pot, you'll be able to tap the pickups. But the usual wiring taps both pickups. There are other options if you want to break from the usual McCarty setup.
One more thing... your pickups (which are wired for the 5-way rotary) will have to be wired a little differently in a McCarty circuit to work properly (click here). The good news is that you can set it so the middle position on the 3-way always gives you Power Out Of Phase (POOP). Many swear by it for clean spanky funk or super-gainy solos.
There are two styles of drop in. One is designed for a McCarty and the other is designed for converting a guitar originally built with a 5 way. As Hans mentioned, the 3 wire McCarty pups and the 4 wire Dragon or HFS pups, require a slightly different approach when installing a toggle with push/pull tone pot.
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