If you are not 100% confident in manual, then absolutely use aperture priority. Make sure you are watching your shutter speed.
As for the small town in ND, that has no bearing on whether you can use flash in the church or not. If it is any of the traditional churches the chances are you cannot use flash during the ceremony. Some of the new ones haven't gotten smart to the flash distraction issues yet and will allow it, but if they've been around more than a couple of years? They're probably on to the whole flash thing by now.
You NEED to go to the church and see what you are going to be working in, take some test shots and know what your problems are going to be. EVERY wedding photographer needs to do it. Failure to do so will result in you having major problems that you can't fix the day of the wedding. Failure to do it is probably the worst thing any wedding photographer could ever do.
Honestly, you're not really ready for this... When is the wedding? How much time do we have to get you ready?