Of course if you are designing a one-off site and aren't interested in learning web design then it may not be appropriate to spend years learning how to do it properly. However, that doesn't mean that we should stop telling you that it is wrong.
I don't mind that you tell me what is wrong, in fact please do, but when it is told to me in such a way that I am stuck like a deer in the headlights and first I have no idea how to fix it and secondly have no idea what is necessary to fix to make it functional vs what is "ok now I know, next time I will do it better".
On my first site I stuck every animated gif I could find only to find that no one visited. Eventually you learn that less is more and any animation on a page is mostly a distraction. A good image with no animation is much better and doesn't take way from the content.
So I don't know if this means: don't use flash banners or never embed movies or what. Ok I do have one animated gif on one page I can change. Got that.
I need to put the movie on the first page. Since it really explains the church and it's vision. Is there a better way to embed it? Should I use something other than .flv?
The top logo is a .png since it really need to be transparent-should I change it to a gif, would that help?? I will certainly work on changing the button .png should they be jpeg or .gif? What about the footer, can you get the same effect (of the pink background going into the picture) some other way?
As far as the main picture should I put the one that I fixed with live text up for now until my brother fixes the main picture (he's in charge of flash, pictures etc.) or just put up text even though it doesn't look so good for a front page?
A page should start with the main heading (h1) and then work down in a logical order with h2 for sub headings and then h3 for sub sub headings etc. You would never follow an h2 with and h5 for example. More info here.
Semantic markup means using the html that is appropriate to the content. As already mentioned above you use a logical heading for headings and for paragraphs you use the p element. For most of the content you put in a page there is ana appropriate html element. (eg. ul for unordered lists, dl for definition lists, table for tabular data, div for block divisions of content or to aid structure (or where there is no suitable html element provided) spans for inline sections where needed and so on...).
the layout breaks horribly on large font/120dpi machines (dynamic fonts in fixed width/height containers)
Are these issues something I need to go through and figure it out and fix it or is this a "now you know better for the next time" issue.
Generally, WYSIWYG editors like the preview pane in Dreamweaver generate disastrous code that rarely if ever works cross browser -- and their 'templates' and 'automatic options' are some of the worst bloated disastrous code out there.
Along the way I certainly figured out that WYSIWYG doesn't always give me what i want and I just need to go into the code and fix it there and open it up in a variety of browsers because it is more realistic. But the basic structure came from a Dreamweaver template.
the CSS how do I take the menuBar css out of the template? and do I need to? what about the two css files I mentioned. Should I do something about that? How do I know what div tags to keep and which ones to get rid of? Do I need to do that now for this website to work?
I probably have a ton more questions that I don't even know I have now.