Its actually quite easy
1st you design your website to be accessible - nothing flash (especially flash!) - simple pages without clutter or special styling only meaningful to your design dept - and doing one job simply on each page, put in in all the WAI bits and pieces and actually work through it several time - test them with someone with disabilities if you can - but blindfolding yourself and using a screenreader is an
eye-opener. You end up with a simple, logical, clean and very easy to maintain set of pages that perform the function they are required to do.
Then maybe style it a bit so it looks pretty (whatever that is this week) and fits into your web site easily.
Then stop because that's all you need to do. Gilding the lilly kills it.