First suggestion is not to make your whole site out of SWiSH, it is very tempting for new users to go over the top and make complete web sites but unfortunately the only ones who will view it will be your friends and family as no one else will wait for it to load!!
Secondly don't use every SWiSH effect possible as this will only bog down your movie and add to loading time, remember your target audience, which will be mostly modem users at this stage I am sure!
Get your ideas down on paper first and create a story board so as you have direction, collect or create your images then assemble, this would be the best approach for you I believe, you could also start a business directory for your church members as no doubt some of them will be business operators, include this in the site to give it some extra functionality...
Yeah, a full Swish site for a church can run you into problems, the main one being having to update info regularly. It's easier to do it in HTML and if you want some flash elements, leave it to a logo, slideshow, that type of thing.