The best way to sync your iPhone to a MC Library is to use iTunes as the sync engine.
Here's a brief review of what I've done...
1. Get prod's great
MC iTunes Sync tool.
2. Make a new Handheld in MC which points to a folder on disk, and select Smartlists for it which will sync your entire library over to the folder (except any stuff which you never want to go onto the phone). This will handle the conversion from unsupported file types (like FLAC and APE and whatnot), and will ensure that iTunes never touches the original source files (and possibly screws up the files).
3. Sync this Handheld over to your folder. Make sure this folder is NOT in your MC Auto-Import path. You don't want these files in MC, only iTunes.
4. In MC, construct a calculated field (ask for help) that will make a field in each file that points to it's corresponding "handheld version" for MCiS. There are instructions for using this feature included with MCiS in the PDF documents.
5. Set up MCiS to only sync this same Smartlist set used in the handheld definition above (this is a command line option for MCiS, again, see the help document).
6. Set MCiS to sync whatever fields you want to persist between the two libraries, and set it up (via the Windows Task Scheduler) to run on a recurring schedule automatically.
If you follow these basic steps, you'll end up with essentially an iTunes Library that is "synced" to your MC library. However, the iTunes Library will point at its own "versions" of the files (which does "cost" extra disk space, but it is worth it for the safety, IMHO). If you set up ONLY that one Handheld in MC, you can even schedule the sync in MC to recur automatically (ask and I can explain how).
Then, you just sync your iDevice to iTunes like normal. It never needs to "touch" MC directly, but you can still keep things like Ratings and Playcounts in sync.
It is challenging to get set up initially, but once you do, it works quite well. I've had mine set up for a LONG time now, and I never really need to touch it. I just have iTunes set to auto-launch-and-sync when I plug in my devices, and it works.
At some point, I'm still planning to build a screencast showing my setup for this in detail, but I've been bogged down working on my auto-conversion system lately.
