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The short answer is yes, you need to pick one and stick with it.
The longer answer is that technically you can switch at any time, but any time you change syncing methods, you'd probably want to sync all your machines, then switch it over on each machine and sync them all again.

One of the main purposes of the local Bonjour sync is to save people from paying for a WebDAV service if they don't need to. If you're already paying for MobileMe or something similar, there may not be much reason to switch to Bonjour syncing. There are only a couple technical advantages to local syncing: (1) It's probably a little faster on average. (2) Your data is not up on some third-party server, which may make you sleep better at night.