I don't have a lot of experience of these things but I did shoot a wedding, once, and learned a lot from some schoolboy errors. So I'll offer some advice but feel free to take it with a pinch of salt. Here goes....
Personally I'd be more concerned about which exposure mode to use rather than which metering mode. I got caught out quite badly when shooting a wedding in Av mode and evaluative metering with a 580EX flash. I don't know how well you know the Canon flash system but it is quite prone to underexpose shots, unless you take steps to compensate, and it will thoughtfully underexpose your background for you to give the flash headroom to illuminate your subject without blowing it out. The unfortunate result is typically underexposure of everything - unless you take charge.
Given that the conditions for shooting a christening in a church will be much the same as for a wedding, here's my advice.....
Use manual exposure. Set ISO to at least 800 and possibly even 1600. Set shutter speed no slower than 1/60. I've seen subject movement ruin shots at that sort of speed and slower - laughter, clapping, anything really, will blur at 1/60 or less. Having IS and/or a monopod will not save you from subject movement. See what sort of aperture you need with that setup. If your lens can open up wide enough, or get within 1 stop of the "correct" exposure then all well and good. You can make up the difference with some flash. With that sort of manual setup the ambient exposure will be taken care of and will not be thrown off by backlighting from windows, lights etc, or thrown off by lights and candles in the foreground.
Now obviously metering is important for the initial setup but really I think you can choose whichever mode you are most comfortable with, take a test shot, chimp the histogram, tweak your manual settings as necessary and then you are pretty much set. Unless the lighting changes you should be able to largely stop worrying about exposure. The flash gun should take care of any little tweaks to foreground/subject lighting but the rest of the church should be sorted. You may need to ride the FEC control a bit if your subject suddenly has a predominance of white/bright tones or a predominance of blacks. The Canon flash system is set up very conservatively to avoid blowing anything, so reflections and specular highlights can trick it into quenching early. Keep a watchful eye on such occurences.
People do say that the flash system is more predictable if you use average flash metering rather than ETTL2. I have found this to be true. If you have the opportunity I suggest you practice with the flash and experiment with different settings to see what works best for you.
That's about all I can offer. I'm afraid in my case it's more theoretical rather than from practical experience but even if I don't know exactly what
to do I certainly know what
not to do!
Here are some tips from a highly regarded guru of flash photography, with some fantastic wedding photographs. May I recommend you browse through his advice on exposure and flash techniques....
http://planetneil.com/tangents/exposure-metering/