Could someone please tell me the advantages and disadvantages of setting my template to 100% as opposed to fixed width and what in peoples opinion is the preferred option?
100% uses the whole screen but keeps your page from horizontal scrolling on smaller monitors. It can look "stretched" on wide monitors unless designed for it. You can use
max-width: 1200px;
to keep the page from over-stretching, although IE6 doesn't support this standard CSS property. (You can also use min-width to keep the page from cramping in tiny windows, with the same caveat.)
Fixed width lets you design for a known page layout and fully control the proportions and relationships of elements.
I would generally go for a fluid width of around 90-95% to give some breathing room, with min- and max-width set so that modern browsers have the best possible range of good function.
If your audience tends to be less tech-savvy and mostly uses IE6, you might want to stick to a fixed width.
There are ways to distinguish what the user is running and adapt your output accordingly; Web design tutorial sites can give info.